Amended Informative Negative Whole Exome Sequencing Results

Amended Informative Negative Whole Exome Sequencing Results | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research article Amended Informative Negative Whole Exome Sequencing Results Lamia Alsubaie, Taghrid Aloraini, Anar Alfarsi, Fuad Al Mutairi, and 9 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-147916/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Background: Whole exome sequencing (WES) is widely used as a first-tier diagnostic test. The diagnostic yield for WES is estimated at approximately 50%, leaving the requesting clinician with 50% ambiguous or negative results in cases where the diseases-causing variants could not be identified. Methods: We retrospectively assessed the results of all WES tests requested from 2015 to 2018 at our institution. We included participants with a negative test result, irrespective of the phenotype. Complete data collection, medical-record extraction, and additional analysis were done for qualifying cases. Results: The cohort included 151 participants with a negative WES result. Of the sample, 18% (n=27) were discharged from the genetic clinic, and only three cases required additional genetic testing prior to discharge. The decision to discharge a patient was based on several factors, including a mild phenotype (i.e. a phenotype that can be resolved and doesn’t require surgical, rehabilitation or medical intervention), a confirmed multifactorial condition, or the patient is developing according to the milestones for his age group and has a negative family history. The discharge rate and the period of being followed at the clinic improved over time. In 2015, none was discharged, and in 2016, nearly 100% of the negative cases were discharged in 6-12 months. In 2017, 65% of the cases were discharged in less than six months, and all cases tested in 2018, were discharged from the clinic in less than three months. Conclusion: Informative negative WES results lower the cost of additional testing, reduce the number of follow-up consultations, and result in the reassurance or discharge the patient. The informative negative WES results (18%) can be combined with the hit rate of the WES (50%) in consanguineous population, increasing the clinical utility of WES testing to 68%. Medical Genetics Molecular Genetics Population Genetics Negative whole exome sequencing informative whole exome sequencing testing whole exome sequencing Figures Figure 1 Background Next generation sequencing (NGS) caused a revolution in genetic research and the clinical diagnosis of human genetic disorders. NGS refers to the deep, high-throughput, in-parallel nucleic acid sequencing technologies that examines multiple genes at the same time (Rabbani, Tekin & Mahdieh 2014 ). NGS technology is currently used in different assays, such as whole genome sequencing (WGS), whole exome sequencing (WES), and targeted gene panels. Of these tests, WES is preferred because it covers more than 85% of disease causing mutations (Rabbani, Tekin & Mahdieh 2014 ), is more cost-effective compared to WGS (Schwarze et al. 2018 ) and the diagnostic yield of WES ranges from 25 to nearly 49% (Alfares et al. 2017 , Yang et al. 2013 , Lee et al. 2014 , Yang et al. 2014 ). Based on these factors, WES is recommended as the first tier testing for suspected genetic disorders (Clark et al. 2018 , Stark et al. 2016 ). Approximately 25–50% of the cases will be identified after the initial genetic testing (i.e. WES), leaving the requesting clinicians with 50–75% ambiguous or negative results. Negative results are defined as the absence of disease causing variants (pathogenic (P) and/or likely pathogenic (LP)) that can fully explain the phenotype. When the variants cannot explain the patient’s phenotype, the results are considered negative. The explanation is that the phenotype is not hereditary, or the genetic cause has not yet been revealed. Re-analysis of the raw data of inconclusive or negative results is recommended for cases that are highly suspicious of an underlying genetic cause before proceeding with further testing (Alfares et al. 2018 , Ewans et al. 2018 ). Management based on a negative result, is completely case-dependent on the patient’s medical and family history. Skinner et al. ( 2016 ) explained that the majority of the negative result interpretations were provisional, and could not rule out genetic diseases. Such results were called nuanced negative. The clinician should interpret the result based on the patient’s phenotype and family data before excluding the possibility of an inherited disorder, as he/she may need to revisit the NGS raw data in future if indicated. However, the result of a negative WES supports reassurance in cases where the phenotype is not significantly linked to a single gene disorder, and with an unremarkable family history. In these cases, a negative result is indeed informative. To add to the knowledge base, we reviewed 151 cases with a negative WES test result and we found that an early negative result optimizes the opportunity to influence the clinical management and discharge patients from the clinic, decreasing costs and the psychological burden on the family and community. Methods We performed a retrospective cohort study of all WES tests conducted from 2015 to 2018 at the genetic clinic at King Abdulaziz Medical City, Riyadh, Saudi Arabia. Only patients with a negative result were included in the study. For the sample, irrespective of their phenotype, complete data were collected and the medical records retrieved, and additional analyses were performed. All WES tests were done in CLIA licensed, CAP certified clinical diagnostic commercial laboratories. The sequencing systems and types of kit are crucial for bioinformatics-pipeline configuration. The generated library is sequenced on Illumina NextSeq or Illumina HiSeq with ~ 100x average depth of coverage, and the minimum coverage for any variant to be considered is 10x. The exclusion criteria were 1) the genetic diagnosis was not obtained by WES but with other tests such as fragile X or methylation analysis, 2) though negative, but with a suspected variant under investigation, 3) patients who declined testing, 4) families where there is a high suspicion of an underlying genetic disorder and the patient is being followed up in the genetic clinic, despite all the negative results. The discharged cases were confirmed by the patient’s geneticist, and the reasons for being discharged were extracted from the electronic health records. Discharge usually occurs when no underlying genetic explanation is identified, or the possible explanation of the phenotype is not likely linked to genetics or the patient’s phenotype improved overtime. All participants gave informed consent for inclusion in the study. The study protocol was approved by the Ethics Committee of the Institutional Research Board of King Abdullah International Medical Research Center (KAIMRC) with a study reference number RC19/315. Results A total of 151 participants with a negative WES result were included. The demographic information of the cohort, as well as detailed clinical phenotype, in the human phenotype ontology (HPO) format, the age at testing, and the NGS results for informative negative cases (n = 27) is available in Table 1 . Table 1 cohort demographics Patient No. Gender Test Type S, D, T, P Date of Testing Phenotype Age at Testing Results Consanguinity First Cousin Family History 1 Male WES Solo 7-Oct-16 Intellectual disability HP:0001249 12.7 Negative No No Yes 2 Male WES Trio 7-Oct-16 Delayed speech and language development HP:0000750, flexion contracture of finger HP:0012785 3.5 Negative No No No 3 Male WES Solo 2-May-17 short stature HP:0004322, Growth hormone deficiency HP:0000824 13.8 Negative Yes Yes Yes 4 Male WES Plus 11-Aug-17 Obesity HP:0001513, Enuresis nocturna HP:0010677 9.7 Negative Yes Yes Yes 5 Female WES Plus 7-Jun-18 ulcerative colitis HP:0100279, constipation HP:0002019, bloody diarrhea HP:0025085 8.6 Negative Yes Yes Yes 6 Male WES Trio 16-Mar-16 Oligohydramnios HP:0001562, Thrombocytopenia HP:0001873, Abnormality of the coagulation cascade HP:0003256, Hydronephrosis HP:0000126, Hypermethioninemia HP:0003235, Hypertyrosinemia HP:0003231, Hypoalbuminemia HP:0003073, Intrahepatic cholestasis with episodic jaundice HP:0006575, Elevated transferrin saturation HP:0012463, Decreased liver function HP:0001410 0.4 Negative No No No 7 Female WES Trio 4-Apr-16 Obesity HP:0001513, Hepatomegaly HP:0002240, Elevated hepatic transaminase HP:0002910 13.1 Negative No No Yes 8 Male WES Trio 28-Jun-16 Cleft palate HP:0000175, feeding difficulties HP:0011968, cough HP:0012735, Abnormality of the ear HP:0000598, Hyperostosis HP:0100774 1.6 Negative No No Yes 9 Male WES Solo 12-Oct-17 Perimembranous ventricular septal defect HP:0011682, Tracheoesophageal fistulaat HP:0002575, Ectopic kidney HP:0000086 1.5 Negative Yes Unknown No 10 Female WES Solo 10-Nov-17 Intellectual disability HP:0001249, obesity HP:0001513, Hyperactivity HP:0000752, Sleep disturbance HP:0002360, Myoclonic seizure HP:0032794 13.3 Negative Yes No No 11 Female WES Duo 23-Nov-17 short stature HP:0004322, Global developmental delay HP:0001263, spasticity HP:0001257, toe walking HP:0040083 14.0 Negative Yes Unknown No 12 Female WES Solo 25-Aug-17 Intellectual disability-mild HP:0001256, failure to thrive HP:0001508, short stature HP:0004322, Abnormal facial shape HP:0001999 14.5 Negative Yes Yes No 13 Male WES Plus 8-Sep-17 Global developmental delay HP:0001263, Delayed speech and language development HP:0000750, Autistic behavior HP:0000729, Attention deficit hyperactivity disorder HP:0007018, Socially inappropriate behavior HP:0030220 7.5 Negative Yes Yes Yes 14 Male WES Plus 24-Apr-18 Atrial septal defect HP:0001631, Delayed speech and language development HP:0000750, Developmental regression HP:0002376, Dysphagia HP:0002015, Global developmental delay HP:0001263, Seizures HP:0001250, Stereotypy HP:0000733 10.2 Negative Yes Unknown Yes 15 Male WES Trio 19-Feb-18 Aggressive behavior HP:0000718, Attention Deficit-hyperactivity Disorder OMIM:143465, behavioral abnormality HP:0000708, Delayed speech and language development HP:0000750, jaundice HP:0000952, lactic aciduria HP:0003648, talipes equinovarus HP:0001762 8.0 Negative Yes Yes No 16 Male WES Trio 21-Jul-18 Abnormality of brainstem morphology HP:0002363, Abnormality of the cerebral ventricles HP:0002118, Abnormality of the corpus callosum HP:0001273, Absent septum pellucidum HP:0001331, Agenesis of corpus callosum HP:0001274, Congenital onset HP:0003577, Global developmental delay HP:0001263 0.9 Negative Yes Unknown No 17 Male WES Solo 11-Jun-18 Delayed speech and language development HP:0000750, short thumb HP:0009778, functional abnormality of the middle ear HP:0011452, abnormal facial shape HP:0001999 5.2 Negative Yes Yes Yes 18 Male WES Trio 7-Jun-18 Autism HP:0000717, Autistic behavior HP:0000729, Delayed speech and language development HP:0000750, Motor delay HP:0001270 6.3 Negative Yes Yes No 19 Male WES Solo 12-Oct-17 Polycystic kidney dysplasia HP:0000113 15.2 Negative Yes Yes Yes 20 Male WES Trio 22-Aug-17 intellectual disability HP:0001249, global developmental delay HP:0001263, motor delay HP:0001270, generalized hypotonia HP:0001290, Joint hypermobility HP:0001382, Abnormal facial shape HP:0001999, Low-set ears HP:0000369, Strabismus HP:0000486, Abnormality of mouth shape HP:0011338, micropenis HP:0000054 10.2 Negative Yes Unknown Yes 21 Male WES Trio 28-Jun-17 Autism HP:0000717, Attention deficit hyperactivity disorder HP:0007018, Macrocephaly HP:0000256, Intellectual disability HP:0001249, Scoliosis HP:0002650 7.3 Negative Yes Yes Yes 22 Male WES Plus 5-Dec-17 Cafe-au-lait spot HP:0000957, Prolonged neonatal jaundice HP:0006579, Abnormal facial shape HP:0001999, Low-set ears HP:0000369, hypertelorism HP:0000316, Aplasia cutis congenita HP:0001057, Thoracic hypoplasia HP:0005257 1.5 Negative No No No 23 Male WES Trio 20-Apr-17 Intrauterine growth retardation HP:0001511, microtia HP:0008551, Abnormal facial shape HP:0001999, Low anterior hairline HP:0000294, low set ears HP:0000369, depressed nasal bridge HP:0005280, Abnormal eye morphology HP:0012372, retrognathia HP:0000278, flat occiput HP:0005469, short neck HP:0000470, brachycephaly HP:0000248 0.8 Negative Yes Yes No 24 Male WES Trio 26-Apr-17 Global developmental delay HP:0001263, Seizures HP:0001250, Spastic diplegia HP:0001264, ventriculomegaly HP:0002119, polyhydramnios HP:0001561, polymicrogyria HP:0002126, cerebellar hypoplasia HP:0001321, Abnormality of the femoral head HP:0003368 8.5 Negative Yes No No 25 Male WES Solo 1-Aug-17 Developmental regression/speech HP:0002376, Intellectual disability HP:0001249 10.8 Negative No No No 26 Female WES Duo 12-Mar-18 Morbid obesity HP:0001513, Short toe HP:0001831, waddling gait HP:0002515 12.6 Negative Yes Yes Yes 27 Male WES Trio 31-May-18 Arthralgia HP:0002829, Corneal dystrophy HP:0001131, Keratoconus HP:0000563, Multiple joint contractures HP:0002828, Scarring HP:0100699 11.7 Negative Yes Unknown Yes The median age of the patients at the time of testing was 6.5 (1 month – 32 years) years. A paediatric patient is defined as a person younger than 14 years. There were only two adult cases. A clinical characteristics analysis was performed on the sample (n = 151). As shown in the supplementary document, a total of 278 phenotypic anomalies, defined by HPO (The Human Phenotype Ontology), were observed in the patients, with global developmental delay the most recurrent feature in 34 of the 151 cases. Five abnormalities, including motor delay, delayed speech and language development, global developmental delay, abnormal facial shape, and hypotonia, were present in 10 patients. Nearly 18% (n = 27) of the cohort has been discharged, based on the negative result of the NGS test (Fig. 1 ). The negative cases were unevenly distributed between the paediatric and adult patients, as 26 of the cases where paediatric patients. The most frequent reason for not reaching a genetic diagnosis, was a mild phenotype (Table 2 ). Only four cases had a confirmed multifactorial condition, defined as diseases caused by more than one factor interacting for instance genetic and environmental factors. These cases have been investigated extensively through the Online Mendelian Inheritance in Man (OMIM), and multifactorial was assigned. For two cases, the patient’s development was according to the milestones expected for his age and there was a negative family history. Of the negative cases, only three cases required additional testing, for example WGS, CMA and MGS prior to discharge. In terms of the WES test type, 12 cases had trio analysis, 8 cases solo analysis, 6 cases trio plus analysis, and 2 cases duo analysis. Table 2 Reason for discharged cases. Reasons for discharged Count Percentage 1. Multifactorial 7 28% 2. Normal development 3 11% 3. Mild phenotype 10 36% 4. All genetic work up is negative 7 25% Total Nuanced WES 27 100% A quarter of the cases (n = 7, 26%) was discharged within a month of releasing the result, and the majority (n = 20, 74%) was discharged within a year of the time of the report. The reason for requiring more time was due to extended molecular testing. In 2015, none of the tested patients were discharged, at the date of this study. All the discharged cases were tested in 2016 to 2018. All the cases (n = 5, 100%) tested in 2016 were discharged within 6 months to one year of testing. In 2017, 14 cases (n = 14) were tested, and three cases (22%) were discharged within one month of testing, six cases (43%) within six months, and five cases (35%) discharged after a year. The last group were patients had a wide range of symptoms affecting different body systems. Interestingly, all cases (n = 8, 100%) tested in 2018, were discharged from the clinic in less than three months. Discussion The study aimed to assess the clinical utility of WES testing to provide effective clinical care and reduce the burden on the healthcare system, and the impact of the negative result on the patient’s management plan. An early and accurate genetic diagnosis could have a major impact on the clinical management, reduce cost and the psychological burden on the family and the community. In this cohort, 18% patients were discharged because their condition is not inherited or it is linked to a complex genetic disorder. This is the first study to assess the usefulness of a negative WES result for the patient and the community. Niguidula et al. ( 2018 ) conducted a survey to evaluate the actions of healthcare providers based on the result of WES and the effect on the medical management of 62 patients. Of the six patients who received a negative result, four were referred to another subspecialty, or discontinued a special diet and an inherited disorder was excluded. They demonstrated that even a negative WES result has an impact on the medical management (Niguidula et al. 2018 ). . Previously, we reported that the paediatric age group is more likely to receive a negative result, 46% compared to 31% in the adult group (Alfares et al. 2020 ). In this study, we report that the paediatric group is more likely to have an informative result, compared to adults and that early testing would assist in a large proportion of children with a negative result, to re-assure the family about the result. Global developmental delay is a broad descriptive medical terminology term. The 2020 ICD-10-CM diagnosis code R62.50 for developmental delay is defined as an unspecified lack of expected normal physiological development in childhood, and the physician usually use this term for different phenotypes. In the current study, we showed that that the reason children with developmental delay have an informative negative result, was because they were healthy or it was unlikely that genetics were the underlying disorder. A milder phenotype can sometimes be difficult to evaluate and would require a long clinical follow-up for reassurance. In this study, we showed that a milder phenotype is the most frequent reason why a patient is discharged from the genetic clinic after receiving a negative result. The negative WES result could lower the cost of additional testing, as of 27 patients with a negative result, only three patients required additional testing, such as WGS or aCGH. However, in 24 patients, the physician was satisfied to use the negative result, with no additional testing and reassure or discharge the patient. This not only lower the cost of testing, but reduce the number of patients being followed up, as almost 18% of the patients were discharged from the clinic due to the negative results. If we add the positive hit rate of the WES in our population ~ 50% (3) to the negative informative cases ~ 18%, the total clinical utility of the WES is ~ 68%. It is noteworthy that there is an increasing trend of physicians being more accepting of a negative result, which may be explained by an increased understanding and confidence in the technology, as well as an improvement in the genetic tools available to support analysis. In conclusion, a negative WES result is an important informative result for patient care and management, and can be an effective tool to re-assure the treating physician and the patient about the possibility of an underlying inherited disorder or that the patient has a mild to no phenotype. Being able to discharge the patient with confidence, reduce the need to follow-up in the clinic or the need for extensive testing. Declarations AVAILABILITY OF DATA AND MATERIAL: The authors declare that the data supporting the findings of this study is available within the paper and its supplementary information files. CONFLICT OF INTEREST The authors declare that they have no competing interests. AUTHORS CONTRIBUTIONS: LA, TA, A.Farsi and A.Alfares designed the study, interpreted the clinical data, and wrote the article. LA, TA, A.Farsi and A.Asinan collected samples, genotyped the cases and helped in statistical analysis. M.A, FA, A.Alswaid, A.Alothaim, and WE contributed in samples collection, clinical correlation and manuscript revision. R.Alniwaider and A.Almuitiri contributed to the WES sequencing pipeline. All authors have read and approved the final manuscripts. And to have agreed both to be personally accountable for the author's own contributions and to ensure that questions related to the accuracy or integrity of any part of the work, even ones in which the author was not personally involved, are appropriately investigated, resolved, and the resolution documented in the literature. ACKNOWLEDGMENT The financial assistance of King Abdullah International Medical Research Centre (KAIMRC) with a study reference number towards this research is hereby acknowledged. References Alfares, A., Aloraini, T., Subaie, L. A., Alissa, A., Qudsi, A. A., Alahmad, A., Mutairi, F. A., Alswaid, A., Alothaim, A., Eyaid, W., Albalwi, M., Alturki, S., & Alfadhel, M. (2018). Whole-genome sequencing offers additional but limited clinical utility compared with reanalysis of whole-exome sequencing. Genetics in medicine : official journal of the American College of Medical Genetics , 20 (11), 1328–1333. https://doi.org/10.1038/gim.2018.41 Alfares, A., Alsubaie, L., Aloraini, T., Alaskar, A., Althagafi, A., Alahmad, A., Rashid, M., Alswaid, A., Alothaim, A., Eyaid, W., Ababneh, F., Albalwi, M., Alotaibi, R., Almutairi, M., Altharawi, N., Alsamer, A., Abdelhakim, M., Kafkas, S., Mineta, K., Cheung, N., … Alfadhel, M. (2020). What is the right sequencing approach? Solo VS extended family analysis in consanguineous populations. BMC medical genomics, 13(1), 103. https://doi.org/10.1186/s12920-020-00743-8 Alfares, A., Alfadhel, M., Wani, T., Alsahli, S., Alluhaydan, I., Al Mutairi, F., Alothaim, A., Albalwi, M., Al Subaie, L., Alturki, S., Al-Twaijri, W., Alrifai, M., Al-Rumayya, A., Alameer, S., Faqeeh, E., Alasmari, A., Alsamman, A., Tashkandia, S., Alghamdi, A., Alhashem, A., … Zada, A. (2017). A multicenter clinical exome study in unselected cohorts from a consanguineous population of Saudi Arabia demonstrated a high diagnostic yield. Molecular genetics and metabolism, 121(2), 91–95. https://doi.org/10.1016/j.ymgme.2017.04.002 Clark, M. M., Stark, Z., Farnaes, L., Tan, T. Y., White, S. M., Dimmock, D., & Kingsmore, S. F. (2018). Meta-analysis of the diagnostic and clinical utility of genome and exome sequencing and chromosomal microarray in children with suspected genetic diseases. NPJ genomic medicine , 3 , 16. https://doi.org/10.1038/s41525-018-0053-8 Ewans, L. J., Schofield, D., Shrestha, R., Zhu, Y., Gayevskiy, V., Ying, K., Walsh, C., Lee, E., Kirk, E. P., Colley, A., Ellaway, C., Turner, A., Mowat, D., Worgan, L., Freckmann, M. L., Lipke, M., Sachdev, R., Miller, D., Field, M., Dinger, M. E., … Roscioli, T. (2018). Whole-exome sequencing reanalysis at 12 months boosts diagnosis and is cost-effective when applied early in Mendelian disorders. Genetics in medicine : official journal of the American College of Medical Genetics , 20 (12), 1564–1574. https://doi.org/10.1038/gim.2018.39 Lee, H., Deignan, J. L., Dorrani, N., Strom, S. P., Kantarci, S., Quintero-Rivera, F., Das, K., Toy, T., Harry, B., Yourshaw, M., Fox, M., Fogel, B. L., Martinez-Agosto, J. A., Wong, D. A., Chang, V. Y., Shieh, P. B., Palmer, C. G., Dipple, K. M., Grody, W. W., Vilain, E., … Nelson, S. F. (2014). Clinical exome sequencing for genetic identification of rare Mendelian disorders. JAMA, 312(18), 1880–1887. https://doi.org/10.1001/jama.2014.14604 Niguidula, N., Alamillo, C., Shahmirzadi Mowlavi, L., Powis, Z., Cohen, J. S., & Farwell Hagman, K. D. (2018). Clinical whole-exome sequencing results impact medical management. Molecular genetics & genomic medicine , 6 (6), 1068–1078. https://doi.org/10.1002/mgg3.484 Rabbani, B., Tekin, M., & Mahdieh, N. (2014). The promise of whole-exome sequencing in medical genetics. Journal of human genetics , 59 (1), 5–15. https://doi.org/10.1038/jhg.2013.114 Skinner, D., Raspberry, K. A., & King, M. (2016). The nuanced negative: Meanings of a negative diagnostic result in clinical exome sequencing. Sociology of health & illness , 38 (8), 1303–1317. https://doi.org/10.1111/1467-9566.12460 Stark, Z., Tan, T. Y., Chong, B., Brett, G. R., Yap, P., Walsh, M., Yeung, A., Peters, H., Mordaunt, D., Cowie, S., Amor, D. J., Savarirayan, R., McGillivray, G., Downie, L., Ekert, P. G., Theda, C., James, P. A., Yaplito-Lee, J., Ryan, M. M., Leventer, R. J., … White, S. M. (2016). A prospective evaluation of whole-exome sequencing as a first-tier molecular test in infants with suspected monogenic disorders. Genetics in medicine : official journal of the American College of Medical Genetics , 18 (11), 1090–1096. https://doi.org/10.1038/gim.2016.1 Schwarze, K., Buchanan, J., Taylor, J. C., & Wordsworth, S. (2018). Are whole-exome and whole-genome sequencing approaches cost-effective? A systematic review of the literature. Genetics in medicine : official journal of the American College of Medical Genetics , 20 (10), 1122–1130. https://doi.org/10.1038/gim.2017.247 Yang, Y., Muzny, D. M., Xia, F., Niu, Z., Person, R., Ding, Y., Ward, P., Braxton, A., Wang, M., Buhay, C., Veeraraghavan, N., Hawes, A., Chiang, T., Leduc, M., Beuten, J., Zhang, J., He, W., Scull, J., Willis, A., Landsverk, M., … Eng, C. M. (2014). Molecular findings among patients referred for clinical whole-exome sequencing. JAMA, 312(18), 1870–1879. https://doi.org/10.1001/jama.2014.14601 Yang, Y., Muzny, D. M., Reid, J. G., Bainbridge, M. N., Willis, A., Ward, P. A., Braxton, A., Beuten, J., Xia, F., Niu, Z., Hardison, M., Person, R., Bekheirnia, M. R., Leduc, M. S., Kirby, A., Pham, P., Scull, J., Wang, M., Ding, Y., Plon, S. E., … Eng, C. M. (2013). Clinical whole-exome sequencing for the diagnosis of mendelian disorders. The New England journal of medicine, 369(16), 1502–1511. https://doi.org/10.1056/NEJMoa1306555 Supplementary data No supplemental data was provided with this version Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-147916","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research article","associatedPublications":[],"authors":[{"id":8259166,"identity":"4ace627f-0db0-4118-a232-f6fafc9a101a","order_by":0,"name":"Lamia Alsubaie","email":"","orcid":"https://orcid.org/0000-0001-8864-8407","institution":"King Abdulaziz Medical City","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Lamia","middleName":"","lastName":"Alsubaie","suffix":""},{"id":8259167,"identity":"61efb525-c61c-4ac4-bbe5-950dc2cdbdcb","order_by":1,"name":"Taghrid Aloraini","email":"","orcid":"","institution":"King Abdulaziz Medical City","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Taghrid","middleName":"","lastName":"Aloraini","suffix":""},{"id":8259168,"identity":"40e98141-1fd5-4dc7-b018-a2e853946c22","order_by":2,"name":"Anar Alfarsi","email":"","orcid":"","institution":"King Abdulaziz Medical City","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Anar","middleName":"","lastName":"Alfarsi","suffix":""},{"id":8259169,"identity":"d0cc16c5-7646-4a19-b455-50dedcaf4977","order_by":3,"name":"Fuad Al Mutairi","email":"","orcid":"","institution":"King Abdulaziz medical city","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Fuad","middleName":"Al","lastName":"Mutairi","suffix":""},{"id":8259170,"identity":"58823687-0808-4a11-acc2-c4d33dbc0b0a","order_by":4,"name":"Abdulrahman Alswaid","email":"","orcid":"","institution":"King Abdulaziz Medical City","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Abdulrahman","middleName":"","lastName":"Alswaid","suffix":""},{"id":8259171,"identity":"bdd55f09-faf1-4ca0-9267-0c11d24af4d0","order_by":5,"name":"Ali Alothaim","email":"","orcid":"","institution":"King Abdulaziz Medical city","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Ali","middleName":"","lastName":"Alothaim","suffix":""},{"id":8259172,"identity":"5e74fbe6-ee2a-4323-be94-62fdb45946ae","order_by":6,"name":"Wafaa Eyaid","email":"","orcid":"","institution":"King Abdulaziz Medical City","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Wafaa","middleName":"","lastName":"Eyaid","suffix":""},{"id":8259173,"identity":"1af81111-d39d-46a8-b8f9-5fc1dc8ca57f","order_by":7,"name":"Mohammed Albalwi","email":"","orcid":"","institution":"King Abdulaziz Medical City","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Mohammed","middleName":"","lastName":"Albalwi","suffix":""},{"id":8259174,"identity":"c483764b-d3d8-48c7-9268-7850f6fb0e97","order_by":8,"name":"Aqila Asinan","email":"","orcid":"","institution":"King Abdulaziz medical city","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Aqila","middleName":"","lastName":"Asinan","suffix":""},{"id":8259175,"identity":"e7faab62-e726-41e0-ae5a-29e67bf7bafc","order_by":9,"name":"Rashed Alniwaider","email":"","orcid":"","institution":"King Abdulaziz Medical City","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Rashed","middleName":"","lastName":"Alniwaider","suffix":""},{"id":8259176,"identity":"9832b4c3-e241-49f9-8b99-c7dad7fbcf68","order_by":10,"name":"Abdulrahman Al Muitiri","email":"","orcid":"","institution":"King Abdulaziz Medical city","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Abdulrahman","middleName":"Al","lastName":"Muitiri","suffix":""},{"id":8259177,"identity":"e55c9652-73c6-419f-ae38-2580997f9696","order_by":11,"name":"Majid Alfadhel","email":"","orcid":"","institution":"King Abdulaziz Medical City","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Majid","middleName":"","lastName":"Alfadhel","suffix":""},{"id":8259178,"identity":"ae77b9ab-a838-4ee2-ae6f-600bfed1560e","order_by":12,"name":"Ahmed Alfares","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAAtElEQVRIiWNgGAWjYBAC9gYg8QHMTCBSC88BBgbGGSRrYeYhTQv72cefbcoOM/Cz5xgw/qghRgtPupl0zrnDDJI9bwyYeY4RocWeIY2NObftMIPBjRwDZgY2Ymzhf8b82RKoxf4GyGH/iNEikcYgzQiyRSLHgIG3jSgtz9gke86l80iceVZwmLePKIelMX/4UWYtx9+evPHhj29EaIEANgZw1BwgWgMDUQE1CkbBKBgFIxcAAAgOLkFdnXs3AAAAAElFTkSuQmCC","orcid":"https://orcid.org/0000-0003-4222-0952","institution":"King Abdulaziz Medical City","correspondingAuthor":true,"submittingAuthor":false,"prefix":"","firstName":"Ahmed","middleName":"","lastName":"Alfares","suffix":""}],"badges":[],"createdAt":"2021-01-14 23:32:21","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-147916/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-147916/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":5103743,"identity":"10719ec3-b4d4-4eb1-b447-e089b72ff6c0","added_by":"auto","created_at":"2021-01-19 22:43:08","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":21505,"visible":true,"origin":"","legend":"breakdown of negative cases. ","description":"","filename":"1.png","url":"https://assets-eu.researchsquare.com/files/rs-147916/v1/b88b805f5fd3a712f1be892a.png"},{"id":13650028,"identity":"85f63b3e-6856-4551-84c7-df7d6bbf34d1","added_by":"auto","created_at":"2021-09-17 09:39:20","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":339713,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-147916/v1/847fb1a4-f5b4-42d4-b84f-a621ea34e5e4.pdf"}],"financialInterests":"","formattedTitle":"\u003cp\u003eAmended Informative Negative Whole Exome Sequencing Results\u003c/p\u003e","fulltext":[{"header":"Background","content":" \u003cp\u003eNext generation sequencing (NGS) caused a revolution in genetic research and the clinical diagnosis of human genetic disorders. NGS refers to the deep, high-throughput, in-parallel nucleic acid sequencing technologies that examines multiple genes at the same time (Rabbani, Tekin \u0026amp; Mahdieh \u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e2014\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eNGS technology is currently used in different assays, such as whole genome sequencing (WGS), whole exome sequencing (WES), and targeted gene panels. Of these tests, WES is preferred because it covers more than 85% of disease causing mutations (Rabbani, Tekin \u0026amp; Mahdieh \u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e2014\u003c/span\u003e), is more cost-effective compared to WGS (Schwarze et al. \u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e2018\u003c/span\u003e) and the diagnostic yield of WES ranges from 25 to nearly 49% (Alfares et al. \u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e2017\u003c/span\u003e, Yang et al. \u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e2013\u003c/span\u003e, Lee et al. \u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e2014\u003c/span\u003e, Yang et al. \u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e2014\u003c/span\u003e ). Based on these factors, WES is recommended as the first tier testing for suspected genetic disorders (Clark et al. \u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e2018\u003c/span\u003e, Stark et al. \u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e2016\u003c/span\u003e). Approximately 25\u0026ndash;50% of the cases will be identified after the initial genetic testing (i.e. WES), leaving the requesting clinicians with 50\u0026ndash;75% ambiguous or negative results. Negative results are defined as the absence of disease causing variants (pathogenic (P) and/or likely pathogenic (LP)) that can fully explain the phenotype. When the variants cannot explain the patient\u0026rsquo;s phenotype, the results are considered negative. The explanation is that the phenotype is not hereditary, or the genetic cause has not yet been revealed. Re-analysis of the raw data of inconclusive or negative results is recommended for cases that are highly suspicious of an underlying genetic cause before proceeding with further testing (Alfares et al. \u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e2018\u003c/span\u003e, Ewans et al. \u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e2018\u003c/span\u003e). Management based on a negative result, is completely case-dependent on the patient\u0026rsquo;s medical and family history. Skinner et al. (\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e2016\u003c/span\u003e) explained that the majority of the negative result interpretations were provisional, and could not rule out genetic diseases. Such results were called nuanced negative. The clinician should interpret the result based on the patient\u0026rsquo;s phenotype and family data before excluding the possibility of an inherited disorder, as he/she may need to revisit the NGS raw data in future if indicated. However, the result of a negative WES supports reassurance in cases where the phenotype is not significantly linked to a single gene disorder, and with an unremarkable family history. In these cases, a negative result is indeed informative.\u003c/p\u003e \u003cp\u003eTo add to the knowledge base, we reviewed 151 cases with a negative WES test result and we found that an early negative result optimizes the opportunity to influence the clinical management and discharge patients from the clinic, decreasing costs and the psychological burden on the family and community.\u003c/p\u003e "},{"header":"Methods","content":" \u003cp\u003eWe performed a retrospective cohort study of all WES tests conducted from 2015 to 2018\u0026nbsp;at the genetic clinic at King Abdulaziz Medical City, Riyadh, Saudi Arabia. Only patients with a negative result were included in the study. For the sample, irrespective of their phenotype, complete data were collected and the medical records retrieved, and additional analyses were performed.\u003c/p\u003e \u003cp\u003eAll WES tests were done in CLIA licensed, CAP certified clinical diagnostic commercial laboratories. The sequencing systems and types of kit are crucial for bioinformatics-pipeline configuration. The generated library is sequenced on Illumina NextSeq or Illumina HiSeq with ~\u0026thinsp;100x average depth of coverage, and the minimum coverage for any variant to be considered is 10x.\u003c/p\u003e \u003cp\u003eThe exclusion criteria were 1) the genetic diagnosis was not obtained by WES but with other tests such as fragile X or methylation analysis, 2) though negative, but with a suspected variant under investigation, 3) patients who declined testing, 4) families where there is a high suspicion of an underlying genetic disorder and the patient is being followed up in the genetic clinic, despite all the negative results.\u003c/p\u003e \u003cp\u003eThe discharged cases were confirmed by the patient\u0026rsquo;s geneticist, and the reasons for being discharged were extracted from the electronic health records. Discharge usually occurs when no underlying genetic explanation is identified, or the possible explanation of the phenotype is not likely linked to genetics or the patient\u0026rsquo;s phenotype improved overtime.\u003c/p\u003e \u003cp\u003eAll participants gave informed consent for inclusion in the study. The study protocol was approved by the Ethics Committee of the Institutional Research Board of King Abdullah International Medical Research Center (KAIMRC) with a study reference number RC19/315.\u003c/p\u003e "},{"header":"Results","content":" \u003cp\u003eA total of 151 participants with a negative WES result were included. The demographic information of the cohort, as well as detailed clinical phenotype, in the human phenotype ontology (HPO) format, the age at testing, and the NGS results for informative negative cases (n\u0026thinsp;=\u0026thinsp;27) is available in Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e.\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab1\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003ecohort demographics\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"11\"\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003ePatient No.\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eGender\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003eTest Type\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003eS, D, T, P\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cp\u003eDate of Testing\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c6\"\u003e \u003cp\u003ePhenotype\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c7\"\u003e \u003cp\u003eAge at Testing\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c8\"\u003e \u003cp\u003eResults\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c9\"\u003e \u003cp\u003eConsanguinity\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c10\"\u003e \u003cp\u003eFirst Cousin\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c11\"\u003e \u003cp\u003eFamily History\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eMale\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eWES\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eSolo\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e7-Oct-16\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eIntellectual disability HP:0001249\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e12.7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eNegative\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eNo\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003eNo\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eMale\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eWES\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eTrio\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e7-Oct-16\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eDelayed speech and language development HP:0000750, flexion contracture of finger HP:0012785\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e3.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eNegative\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eNo\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003eNo\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003eNo\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eMale\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eWES\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eSolo\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e2-May-17\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eshort stature HP:0004322, Growth hormone deficiency HP:0000824\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e13.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eNegative\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eMale\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eWES\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003ePlus\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e11-Aug-17\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eObesity HP:0001513, Enuresis nocturna HP:0010677\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e9.7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eNegative\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eFemale\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eWES\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003ePlus\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e7-Jun-18\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eulcerative colitis HP:0100279, constipation HP:0002019, bloody diarrhea HP:0025085\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e8.6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eNegative\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eMale\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eWES\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eTrio\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e16-Mar-16\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eOligohydramnios HP:0001562, Thrombocytopenia HP:0001873, Abnormality of the coagulation cascade HP:0003256, Hydronephrosis HP:0000126, Hypermethioninemia HP:0003235, Hypertyrosinemia HP:0003231, Hypoalbuminemia HP:0003073, Intrahepatic cholestasis with episodic jaundice HP:0006575, Elevated transferrin saturation HP:0012463, Decreased liver function HP:0001410\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e0.4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eNegative\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eNo\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003eNo\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003eNo\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eFemale\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eWES\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eTrio\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e4-Apr-16\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eObesity HP:0001513, Hepatomegaly HP:0002240, Elevated hepatic transaminase HP:0002910\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e13.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eNegative\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eNo\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003eNo\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eMale\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eWES\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eTrio\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e28-Jun-16\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eCleft palate HP:0000175, feeding difficulties HP:0011968, cough HP:0012735, Abnormality of the ear HP:0000598, Hyperostosis HP:0100774\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e1.6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eNegative\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eNo\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003eNo\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eMale\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eWES\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eSolo\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e12-Oct-17\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003ePerimembranous ventricular septal defect HP:0011682, Tracheoesophageal fistulaat HP:0002575, Ectopic kidney HP:0000086\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e1.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eNegative\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003eUnknown\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003eNo\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e10\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eFemale\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eWES\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eSolo\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e10-Nov-17\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eIntellectual disability HP:0001249, obesity HP:0001513, Hyperactivity HP:0000752, Sleep disturbance HP:0002360, Myoclonic seizure HP:0032794\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e13.3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eNegative\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003eNo\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003eNo\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e11\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eFemale\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eWES\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eDuo\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e23-Nov-17\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eshort stature HP:0004322, Global developmental delay HP:0001263, spasticity HP:0001257, toe walking HP:0040083\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e14.0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eNegative\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003eUnknown\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003eNo\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e12\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eFemale\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eWES\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eSolo\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e25-Aug-17\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eIntellectual disability-mild HP:0001256, failure to thrive HP:0001508, short stature HP:0004322, Abnormal facial shape HP:0001999\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e14.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eNegative\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003eNo\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eMale\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eWES\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003ePlus\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e8-Sep-17\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eGlobal developmental delay HP:0001263, Delayed speech and language development HP:0000750, Autistic behavior HP:0000729, Attention deficit hyperactivity disorder HP:0007018, Socially inappropriate behavior HP:0030220\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e7.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eNegative\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e14\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eMale\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eWES\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003ePlus\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e24-Apr-18\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eAtrial septal defect HP:0001631, Delayed speech and language development HP:0000750, Developmental regression HP:0002376, Dysphagia HP:0002015, Global developmental delay HP:0001263, Seizures HP:0001250, Stereotypy HP:0000733\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e10.2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eNegative\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003eUnknown\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e15\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eMale\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eWES\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eTrio\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e19-Feb-18\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eAggressive behavior HP:0000718, Attention Deficit-hyperactivity Disorder OMIM:143465, behavioral abnormality HP:0000708, Delayed speech and language development HP:0000750, jaundice HP:0000952, lactic aciduria HP:0003648, talipes equinovarus HP:0001762\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e8.0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eNegative\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003eNo\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e16\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eMale\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eWES\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eTrio\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e21-Jul-18\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eAbnormality of brainstem morphology HP:0002363, Abnormality of the cerebral ventricles HP:0002118, Abnormality of the corpus callosum HP:0001273, Absent septum pellucidum HP:0001331, Agenesis of corpus callosum HP:0001274, Congenital onset HP:0003577, Global developmental delay HP:0001263\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e0.9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eNegative\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003eUnknown\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003eNo\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e17\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eMale\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eWES\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eSolo\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e11-Jun-18\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eDelayed speech and language development HP:0000750, short thumb HP:0009778, functional abnormality of the middle ear HP:0011452, abnormal facial shape HP:0001999\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e5.2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eNegative\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e18\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eMale\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eWES\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eTrio\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e7-Jun-18\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eAutism HP:0000717, Autistic behavior HP:0000729, Delayed speech and language development HP:0000750, Motor delay HP:0001270\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e6.3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eNegative\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003eNo\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e19\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eMale\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eWES\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eSolo\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e12-Oct-17\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003ePolycystic kidney dysplasia HP:0000113\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e15.2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eNegative\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e20\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eMale\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eWES\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eTrio\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e22-Aug-17\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eintellectual disability HP:0001249, global developmental\u003c/p\u003e \u003cp\u003edelay HP:0001263, motor delay HP:0001270, generalized hypotonia HP:0001290, Joint hypermobility HP:0001382, Abnormal facial shape HP:0001999, Low-set ears HP:0000369, Strabismus HP:0000486, Abnormality of mouth shape HP:0011338, micropenis HP:0000054\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e10.2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eNegative\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003eUnknown\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e21\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eMale\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eWES\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eTrio\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e28-Jun-17\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eAutism HP:0000717, Attention deficit hyperactivity disorder HP:0007018, Macrocephaly HP:0000256, Intellectual disability HP:0001249, Scoliosis HP:0002650\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e7.3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eNegative\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e22\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eMale\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eWES\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003ePlus\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e5-Dec-17\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eCafe-au-lait spot HP:0000957, Prolonged neonatal jaundice HP:0006579, Abnormal facial shape HP:0001999, Low-set ears HP:0000369, hypertelorism HP:0000316, Aplasia cutis congenita HP:0001057, Thoracic hypoplasia HP:0005257\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e1.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eNegative\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eNo\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003eNo\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003eNo\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e23\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eMale\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eWES\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eTrio\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e20-Apr-17\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eIntrauterine growth retardation HP:0001511, microtia HP:0008551, Abnormal facial shape HP:0001999, Low anterior hairline HP:0000294, low set ears HP:0000369, depressed nasal bridge HP:0005280, Abnormal eye morphology HP:0012372, retrognathia HP:0000278, flat occiput HP:0005469, short neck HP:0000470, brachycephaly HP:0000248\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e0.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eNegative\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003eNo\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e24\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eMale\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eWES\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eTrio\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e26-Apr-17\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eGlobal developmental delay HP:0001263, Seizures HP:0001250, Spastic diplegia HP:0001264, ventriculomegaly HP:0002119, polyhydramnios HP:0001561, polymicrogyria HP:0002126, cerebellar hypoplasia HP:0001321, Abnormality of the femoral head HP:0003368\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e8.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eNegative\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003eNo\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003eNo\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e25\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eMale\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eWES\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eSolo\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e1-Aug-17\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eDevelopmental regression/speech HP:0002376, Intellectual disability HP:0001249\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e10.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eNegative\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eNo\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003eNo\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003eNo\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e26\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eFemale\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eWES\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eDuo\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e12-Mar-18\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eMorbid obesity HP:0001513, Short toe HP:0001831, waddling gait HP:0002515\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e12.6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eNegative\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e27\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eMale\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eWES\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eTrio\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e31-May-18\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eArthralgia HP:0002829, Corneal dystrophy HP:0001131, Keratoconus HP:0000563, Multiple joint contractures HP:0002828, Scarring HP:0100699\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e11.7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eNegative\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003eUnknown\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003eYes\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003cp\u003eThe median age of the patients at the time of testing was 6.5 (1\u0026nbsp;month \u0026ndash; 32\u0026nbsp;years) years. A paediatric patient is defined as a person younger than 14\u0026nbsp;years. There were only two adult cases.\u003c/p\u003e \u003cp\u003eA clinical characteristics analysis was performed on the sample (n\u0026thinsp;=\u0026thinsp;151). As shown in the supplementary document, a total of 278 phenotypic anomalies, defined by HPO (The Human Phenotype Ontology), were observed in the patients, with global developmental delay the most recurrent feature in 34 of the 151 cases. Five abnormalities, including motor delay, delayed speech and language development, global developmental delay, abnormal facial shape, and hypotonia, were present in 10 patients.\u003c/p\u003e \u003cp\u003eNearly 18% (n\u0026thinsp;=\u0026thinsp;27) of the cohort has been discharged, based on the negative result of the NGS test (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). The negative cases were unevenly distributed between the paediatric and adult patients, as 26 of the cases where paediatric patients.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eThe most frequent reason for not reaching a genetic diagnosis, was a mild phenotype (Table\u0026nbsp;\u003cspan refid=\"Tab2\" class=\"InternalRef\"\u003e2\u003c/span\u003e). Only four cases had a confirmed multifactorial condition, defined as diseases caused by more than one factor interacting for instance genetic and environmental factors. These cases have been investigated extensively through the Online Mendelian Inheritance in Man (OMIM), and multifactorial was assigned. For two cases, the patient\u0026rsquo;s development was according to the milestones expected for his age and there was a negative family history. Of the negative cases, only three cases required additional testing, for example WGS, CMA and MGS prior to discharge. In terms of the WES test type, 12 cases had trio analysis, 8 cases solo analysis, 6 cases trio plus analysis, and 2 cases duo analysis.\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab2\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 2\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eReason for discharged cases.\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"4\"\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\" morerows=\"5\" rowspan=\"6\"\u003e \u003cp\u003eReasons for discharged\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eCount\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003ePercentage\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e1. Multifactorial\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e28%\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e2. Normal development\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e11%\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e3. Mild phenotype\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e10\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e36%\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e4. All genetic work up is negative\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e25%\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eTotal Nuanced WES\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e27\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e100%\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003cp\u003eA quarter of the cases (n\u0026thinsp;=\u0026thinsp;7, 26%) was discharged within a month of releasing the result, and the majority (n\u0026thinsp;=\u0026thinsp;20, 74%) was discharged within a year of the time of the report. The reason for requiring more time was due to extended molecular testing.\u003c/p\u003e \u003cp\u003eIn 2015, none of the tested patients were discharged, at the date of this study. All the discharged cases were tested in 2016 to 2018. All the cases (n\u0026thinsp;=\u0026thinsp;5, 100%) tested in 2016 were discharged within 6\u0026nbsp;months to one year of testing. In 2017, 14 cases (n\u0026thinsp;=\u0026thinsp;14) were tested, and three cases (22%) were discharged within one month of testing, six cases (43%) within six months, and five cases (35%) discharged after a year. The last group were patients had a wide range of symptoms affecting different body systems. Interestingly, all cases (n\u0026thinsp;=\u0026thinsp;8, 100%) tested in 2018, were discharged from the clinic in less than three months.\u003c/p\u003e "},{"header":"Discussion","content":" \u003cp\u003eThe study aimed to assess the clinical utility of WES testing to provide effective clinical care and reduce the burden on the healthcare system, and the impact of the negative result on the patient\u0026rsquo;s management plan. An early and accurate genetic diagnosis could have a major impact on the clinical management, reduce cost and the psychological burden on the family and the community. In this cohort, 18% patients were discharged because their condition is not inherited or it is linked to a complex genetic disorder. This is the first study to assess the usefulness of a negative WES result for the patient and the community. Niguidula et al. (\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e2018\u003c/span\u003e) conducted a survey to evaluate the actions of healthcare providers based on the result of WES and the effect on the medical management of 62 patients. Of the six patients who received a negative result, four were referred to another subspecialty, or discontinued a special diet and an inherited disorder was excluded. They demonstrated that even a negative WES result has an impact on the medical management (Niguidula et al. \u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e2018\u003c/span\u003e). .\u003c/p\u003e \u003cp\u003ePreviously, we reported that the paediatric age group is more likely to receive a negative result, 46% compared to 31% in the adult group (Alfares et al. \u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2020\u003c/span\u003e). In this study, we report that the paediatric group is more likely to have an informative result, compared to adults and that early testing would assist in a large proportion of children with a negative result, to re-assure the family about the result.\u003c/p\u003e \u003cp\u003eGlobal developmental delay is a broad descriptive medical terminology term. The 2020 ICD-10-CM diagnosis code R62.50 for developmental delay is defined as an unspecified lack of expected normal physiological development in childhood, and the physician usually use this term for different phenotypes. In the current study, we showed that that the reason children with developmental delay have an informative negative result, was because they were healthy or it was unlikely that genetics were the underlying disorder.\u003c/p\u003e \u003cp\u003eA milder phenotype can sometimes be difficult to evaluate and would require a long clinical follow-up for reassurance. In this study, we showed that a milder phenotype is the most frequent reason why a patient is discharged from the genetic clinic after receiving a negative result.\u003c/p\u003e \u003cp\u003eThe negative WES result could lower the cost of additional testing, as of 27 patients with a negative result, only three patients required additional testing, such as WGS or aCGH. However, in 24 patients, the physician was satisfied to use the negative result, with no additional testing and reassure or discharge the patient. This not only lower the cost of testing, but reduce the number of patients being followed up, as almost 18% of the patients were discharged from the clinic due to the negative results. If we add the positive hit rate of the WES in our population\u0026thinsp;~\u0026thinsp;50% (3) to the negative informative cases\u0026thinsp;~\u0026thinsp;18%, the total clinical utility of the WES is ~\u0026thinsp;68%. It is noteworthy that there is an increasing trend of physicians being more accepting of a negative result, which may be explained by an increased understanding and confidence in the technology, as well as an improvement in the genetic tools available to support analysis.\u003c/p\u003e \u003cp\u003eIn conclusion, a negative WES result is an important informative result for patient care and management, and can be an effective tool to re-assure the treating physician and the patient about the possibility of an underlying inherited disorder or that the patient has a mild to no phenotype. Being able to discharge the patient with confidence, reduce the need to follow-up in the clinic or the need for extensive testing.\u003c/p\u003e "},{"header":"Declarations","content":"\u003cp\u003eAVAILABILITY OF DATA AND MATERIAL:\u003c/p\u003e\n\u003cp\u003eThe authors declare that the data supporting the findings of this study is available within the paper and its supplementary information files.\u003c/p\u003e\n\u003cp\u003eCONFLICT OF INTEREST\u003c/p\u003e\n\u003cp\u003eThe authors declare that they have no competing interests.\u003c/p\u003e\n\u003cp\u003eAUTHORS CONTRIBUTIONS:\u003c/p\u003e\n\u003cp\u003eLA, TA, A.Farsi and A.Alfares designed the study, interpreted the clinical data, and wrote the article. LA, TA, A.Farsi and A.Asinan collected samples, genotyped the cases and helped in statistical analysis. M.A, FA, A.Alswaid, A.Alothaim, and WE contributed in samples collection, clinical correlation and manuscript revision. R.Alniwaider and A.Almuitiri contributed to the WES sequencing pipeline. All authors have read and approved the final manuscripts. And to have agreed both to be personally accountable for the author's own contributions and to ensure that questions related to the accuracy or integrity of any part of the work, even ones in which the author was not personally involved, are appropriately investigated, resolved, and the resolution documented in the literature.\u003c/p\u003e\n\u003cp\u003eACKNOWLEDGMENT\u003c/p\u003e\n\u003cp\u003eThe financial assistance of King Abdullah International Medical Research Centre (KAIMRC) with a study reference number towards this research is hereby acknowledged.\u003c/p\u003e"},{"header":"References","content":"\u003cp\u003eAlfares, A., Aloraini, T., Subaie, L. A., Alissa, A., Qudsi, A. A., Alahmad, A., Mutairi, F. A., Alswaid, A., Alothaim, A., Eyaid, W., Albalwi, M., Alturki, S., \u0026amp; Alfadhel, M. (2018). Whole-genome sequencing offers additional but limited clinical utility compared with reanalysis of whole-exome sequencing.\u0026nbsp;\u003cem\u003eGenetics in medicine : official journal of the American College of Medical Genetics\u003c/em\u003e,\u0026nbsp;\u003cem\u003e20\u003c/em\u003e(11), 1328\u0026ndash;1333. https://doi.org/10.1038/gim.2018.41\u003c/p\u003e\n\u003cp\u003eAlfares, A., Alsubaie, L., Aloraini, T., Alaskar, A., Althagafi, A., Alahmad, A., Rashid, M., Alswaid, A., Alothaim, A., Eyaid, W., Ababneh, F., Albalwi, M., Alotaibi, R., Almutairi, M., Altharawi, N., Alsamer, A., Abdelhakim, M., Kafkas, S., Mineta, K., Cheung, N., \u0026hellip; Alfadhel, M. (2020). What is the right sequencing approach? Solo VS extended family analysis in consanguineous populations. BMC medical genomics, 13(1), 103. https://doi.org/10.1186/s12920-020-00743-8\u003c/p\u003e\n\u003cp\u003eAlfares, A., Alfadhel, M., Wani, T., Alsahli, S., Alluhaydan, I., Al Mutairi, F., Alothaim, A., Albalwi, M., Al Subaie, L., Alturki, S., Al-Twaijri, W., Alrifai, M., Al-Rumayya, A., Alameer, S., Faqeeh, E., Alasmari, A., Alsamman, A., Tashkandia, S., Alghamdi, A., Alhashem, A., \u0026hellip; Zada, A. (2017). A multicenter clinical exome study in unselected cohorts from a consanguineous population of Saudi Arabia demonstrated a high diagnostic yield. Molecular genetics and metabolism, 121(2), 91\u0026ndash;95. https://doi.org/10.1016/j.ymgme.2017.04.002\u003c/p\u003e\n\u003cp\u003eClark, M. M., Stark, Z., Farnaes, L., Tan, T. Y., White, S. M., Dimmock, D., \u0026amp; Kingsmore, S. F. (2018). Meta-analysis of the diagnostic and clinical utility of genome and exome sequencing and chromosomal microarray in children with suspected genetic diseases.\u0026nbsp;\u003cem\u003eNPJ genomic medicine\u003c/em\u003e,\u0026nbsp;\u003cem\u003e3\u003c/em\u003e, 16. https://doi.org/10.1038/s41525-018-0053-8\u003c/p\u003e\n\u003cp\u003eEwans, L. J., Schofield, D., Shrestha, R., Zhu, Y., Gayevskiy, V., Ying, K., Walsh, C., Lee, E., Kirk, E. P., Colley, A., Ellaway, C., Turner, A., Mowat, D., Worgan, L., Freckmann, M. L., Lipke, M., Sachdev, R., Miller, D., Field, M., Dinger, M. E., \u0026hellip; Roscioli, T. (2018). Whole-exome sequencing reanalysis at 12 months boosts diagnosis and is cost-effective when applied early in Mendelian disorders.\u0026nbsp;\u003cem\u003eGenetics in medicine : official journal of the American College of Medical Genetics\u003c/em\u003e,\u0026nbsp;\u003cem\u003e20\u003c/em\u003e(12), 1564\u0026ndash;1574. https://doi.org/10.1038/gim.2018.39\u003c/p\u003e\n\u003cp\u003eLee, H., Deignan, J. L., Dorrani, N., Strom, S. P., Kantarci, S., Quintero-Rivera, F., Das, K., Toy, T., Harry, B., Yourshaw, M., Fox, M., Fogel, B. L., Martinez-Agosto, J. A., Wong, D. A., Chang, V. Y., Shieh, P. B., Palmer, C. G., Dipple, K. M., Grody, W. W., Vilain, E., \u0026hellip; Nelson, S. F. (2014). Clinical exome sequencing for genetic identification of rare Mendelian disorders. JAMA, 312(18), 1880\u0026ndash;1887. https://doi.org/10.1001/jama.2014.14604\u003c/p\u003e\n\u003cp\u003eNiguidula, N., Alamillo, C., Shahmirzadi Mowlavi, L., Powis, Z., Cohen, J. S., \u0026amp; Farwell Hagman, K. D. (2018). Clinical whole-exome sequencing results impact medical management.\u0026nbsp;\u003cem\u003eMolecular genetics \u0026amp; genomic medicine\u003c/em\u003e,\u0026nbsp;\u003cem\u003e6\u003c/em\u003e(6), 1068\u0026ndash;1078. https://doi.org/10.1002/mgg3.484\u003c/p\u003e\n\u003cp\u003eRabbani, B., Tekin, M., \u0026amp; Mahdieh, N. (2014). The promise of whole-exome sequencing in medical genetics.\u0026nbsp;\u003cem\u003eJournal of human genetics\u003c/em\u003e,\u0026nbsp;\u003cem\u003e59\u003c/em\u003e(1), 5\u0026ndash;15. https://doi.org/10.1038/jhg.2013.114\u003c/p\u003e\n\u003cp\u003eSkinner, D., Raspberry, K. A., \u0026amp; King, M. (2016). The nuanced negative: Meanings of a negative diagnostic result in clinical exome sequencing.\u0026nbsp;\u003cem\u003eSociology of health \u0026amp; illness\u003c/em\u003e,\u0026nbsp;\u003cem\u003e38\u003c/em\u003e(8), 1303\u0026ndash;1317. https://doi.org/10.1111/1467-9566.12460\u003c/p\u003e\n\u003cp\u003eStark, Z., Tan, T. Y., Chong, B., Brett, G. R., Yap, P., Walsh, M., Yeung, A., Peters, H., Mordaunt, D., Cowie, S., Amor, D. J., Savarirayan, R., McGillivray, G., Downie, L., Ekert, P. G., Theda, C., James, P. A., Yaplito-Lee, J., Ryan, M. M., Leventer, R. J., \u0026hellip; White, S. M. (2016). A prospective evaluation of whole-exome sequencing as a first-tier molecular test in infants with suspected monogenic disorders.\u0026nbsp;\u003cem\u003eGenetics in medicine : official journal of the American College of Medical Genetics\u003c/em\u003e,\u0026nbsp;\u003cem\u003e18\u003c/em\u003e(11), 1090\u0026ndash;1096. https://doi.org/10.1038/gim.2016.1\u003c/p\u003e\n\u003cp\u003eSchwarze, K., Buchanan, J., Taylor, J. C., \u0026amp; Wordsworth, S. (2018). Are whole-exome and whole-genome sequencing approaches cost-effective? A systematic review of the literature.\u0026nbsp;\u003cem\u003eGenetics in medicine : official journal of the American College of Medical Genetics\u003c/em\u003e,\u0026nbsp;\u003cem\u003e20\u003c/em\u003e(10), 1122\u0026ndash;1130. https://doi.org/10.1038/gim.2017.247\u003c/p\u003e\n\u003cp\u003eYang, Y., Muzny, D. M., Xia, F., Niu, Z., Person, R., Ding, Y., Ward, P., Braxton, A., Wang, M., Buhay, C., Veeraraghavan, N., Hawes, A., Chiang, T., Leduc, M., Beuten, J., Zhang, J., He, W., Scull, J., Willis, A., Landsverk, M., \u0026hellip; Eng, C. M. (2014). Molecular findings among patients referred for clinical whole-exome sequencing. JAMA, 312(18), 1870\u0026ndash;1879. https://doi.org/10.1001/jama.2014.14601\u003c/p\u003e\n\u003cp\u003eYang, Y., Muzny, D. M., Reid, J. G., Bainbridge, M. N., Willis, A., Ward, P. A., Braxton, A., Beuten, J., Xia, F., Niu, Z., Hardison, M., Person, R., Bekheirnia, M. R., Leduc, M. S., Kirby, A., Pham, P., Scull, J., Wang, M., Ding, Y., Plon, S. E., \u0026hellip; Eng, C. M. (2013). Clinical whole-exome sequencing for the diagnosis of mendelian disorders. The New England journal of medicine, 369(16), 1502\u0026ndash;1511. https://doi.org/10.1056/NEJMoa1306555\u003c/p\u003e"},{"header":"Supplementary data","content":"\u003cp\u003eNo supplemental data was provided with this version\u003c/p\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"Negative whole exome sequencing, informative whole exome sequencing, testing whole exome sequencing ","lastPublishedDoi":"10.21203/rs.3.rs-147916/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-147916/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eBackground: Whole exome sequencing (WES) is widely used as a first-tier diagnostic test. The diagnostic yield for WES is estimated at approximately 50%, leaving the requesting clinician with 50% ambiguous or negative results in cases where the diseases-causing variants could not be identified.\u0026nbsp;\u003c/p\u003e\u003cp\u003eMethods: We retrospectively assessed the results of all WES tests requested from 2015 to 2018 at our institution. We included participants with a negative test result, irrespective of the phenotype. Complete data collection, medical-record extraction, and additional analysis were done for qualifying cases. \u003c/p\u003e\u003cp\u003eResults: The cohort included 151 participants with a negative WES result. Of the sample, 18% (n=27) were discharged from the genetic clinic, and only three cases required additional genetic testing prior to discharge. The decision to discharge a patient was based on several factors, including a mild phenotype (i.e. a phenotype that can be resolved and doesn’t require surgical, rehabilitation or medical intervention), a confirmed multifactorial condition, or the patient is developing according to the milestones for his age group and has a negative family history.\u0026nbsp;The discharge rate and the period of being followed at the clinic improved over time. In 2015, none was discharged, and in 2016, nearly 100% of the negative cases were discharged in 6-12 months. In 2017, 65% of the cases were discharged in less than six months, and all cases tested in 2018, were discharged from the clinic in less than three months.\u003c/p\u003e\u003cp\u003eConclusion: Informative negative WES results lower the cost of additional testing, reduce the number of follow-up consultations, and result in the reassurance or discharge the patient. The informative negative WES results (18%) can be combined with the hit rate of the WES (50%) in consanguineous population, increasing the clinical utility of WES testing to 68%. \u0026nbsp;\u003c/p\u003e","manuscriptTitle":"Amended Informative Negative Whole Exome Sequencing Results","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2021-01-19 22:43:06","doi":"10.21203/rs.3.rs-147916/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"838c820b-8eba-4b46-9b1f-95126caa0271","owner":[],"postedDate":"January 19th, 2021","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[{"id":1937423,"name":"Medical Genetics"},{"id":1937424,"name":"Molecular Genetics"},{"id":1937425,"name":"Population Genetics"}],"tags":[],"updatedAt":"2021-01-19T22:43:06+00:00","versionOfRecord":[],"versionCreatedAt":"2021-01-19 22:43:06","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-147916","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-147916","identity":"rs-147916","version":["v1"]},"buildId":"7rjqhiLT3MXkJMwkYKINL","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}