Currently recognized clinically relevant and known genes for human reproduction and related infertility with representation on high-resolution chromosome ideograms.

We developed high resolution chromosome ideograms at the 850 band level and plotted the location of the gene symbol representing each gene onto the ideogram at the precise chromosome band or subband level for each of the 371 genes reported to play a role in human infertility and/or reproduction. The genes were identified by searching the medical literature and computer-based websites. Clinically relevant or known human infertility and/or reproductive genes were found to be distributed on all chromosomes ( Fig. 1 ). Not surprisingly, the largest percentage of human reproduction and related infertility genes (i.e., 59 of 371 genes or 16%) were located on the sex chromosome pair (i.e., X and Y) in relationship to the autosomes or non-sex chromosomes. The gene symbol, expanded name and chromosome location are listed in alphabetical order in Table 1 for each of the 371 human infertility and/or reproductive genes. These genes represented a wide range of functions including sex hormone, peptide receptors, organ development, growth, gene transcription or translational factors, germ cell production and metabolic or neuronal influences ( Venkatesh et al., 2014 ; Layman, 2002 ; Okada et al., 2010 , Hu et al., 2014 ; Kosova et al., 2012 ; El Inati et al., 2012 ; Qiu et al., 2013 ; Ferfouri et al., 2013 ; Albertsen et al., 2013 ; Brannian and Hansen, 2002 ; Fragouli et al., 2014 ; Bulun, 2014 ; Greene et al., 2014 ; Qin et al., 2014 ; Abid et al., 2013 ; Bergh et al., 1993 ). The GeneAnalytics program identified 5 superpathways with a significant number of overlapping genes in the compiled list of human reproduction and related infertility genes. The Ovarian Steroidogenesis superpathway received the most significant score (score = 80.2) with 23 out of a total gene set of 51 included on our master list of reproduction genes. Genes associated with 16 disease processes showed significant overlap. The top five diseases were Prostate Cancer (32 out of 313, score = 28.6), Infertility (21 out of 22, score = 25.5), Breast Cancer (32 out of 781, score = 24.8), Obesity (29 out of 576, score = 21.7) and Lung Cancer (30 out of 622, score = 21.0). Significant overlap related to tissue and cell type was found for the testis (124 out of 3818, score = 16.6). Multiple overlapping pathways for biological (27 pathways) and molecular (5 pathways) processes were identified that significantly impacted spermatogenesis, male gonad development, cell differentiation and organismal development involving steroidogenesis, hormone receptor activity, sequence-specific DNA and protein binding. These pathways point to functional roles in cellular growth and development targeting gonadal development, maturation and function as key underlying genetic architecture for reproduction and related infertility. We summarized evidence from the peer-reviewed medical literature using computer-based search engine websites for genes playing a definitive role in human infertility and reproduction. We thus provided an update on the list of 153 relevant genes in human reproduction and/or infertility that was reported previously ( Butler et al., 2015 ). This updated list includes a total of 371 clinically relevant and known genes for human infertility and/or reproduction. We also provided a pictorial image of the location and distribution of genes on high resolution chromosome ideograms. Not surprisingly, a preponderance of human reproduction and related infertility genes were found on the sex chromosome pair in relationship to the 22 pairs of autosomes which include 68 genes primarily impacting testis formation or sperm production with 24 located on the Y chromosome and 5 on the X chromosome. Genes that directly influence reproduction or infertility are also involved with testes function and spermatogonial cell production (e.g., ETV5, SPACA1, TSSK6) , premature ovarian failure (e.g., FMR1) or primary ovarian insufficiency (e.g., SHOX, CCNH, HSD3B2, GNAS) , development of obesity or susceptibility (e.g., FTO, PCSIK,STAR) , gene expression or transcription activators (e.g., NFE2L3) or other transcription and translation factors (e.g., CRTC1, TCEB3B, NUPR1, EIF2B2) required for the proper development of somatotrophs, thyrotrophs and gonadotrophs (e.g., PROP1) , organization or function of the endoplasmic reticulum and protein export (e.g., SEC16B ) or recycling (e.g., MAGEL2) , testes-specific RNA splicing factors (e.g., TRA2B ) and transcription factors involved with genito-urinary or gonad development (e.g., WT1, CFTR ) [genes reviewed in Online Mendelian Inheritance in Man ( www.OMIM.org ) and in Gene Cards ( www.genecards.org )]. Collectively, our list of reproduction and infertility genes impact common hormone pathways encompassing ovarian steroidogenesis along with related peptide production and their receptors, specifically those required for hormone storage and transport, gonadal structure and function and germ cell development as noted in Table 1 . These roles also directly influence cellular growth and development relevant to disease states involving cancer risk for multiple cell types (prostate, breast, lung and colon). Data from genome-wide association studies (GWAS) have shown that the onset of menarche in females is influenced by at least 35 individual genes ( Qiu et al., 2013 ; Montgomery et al., 2014 ). These include FTO, TRA2B, ETV5, TMEM18 and SEC16B which are also known as obesity-related genes ( Choquet and Meyre, 2011a , 2011b ; Speliotes et al., 2010 ; Scherag et al., 2010 ). Pathways analysis of our tabulated list of human reproduction and infertility genes also identified significant overlap with the Obesity disease state. An example of an obesity-related disorder that is characterized by menstrual irregularities, hyperandrogenism and subfertility is polycystic ovary syndrome (PCOS). About 50% of women with PCOS are also obese ( Pasquali and Gambineri, 2006 ; Erhmann, 2005) with several genes implicated ( Venkatesh et al., 2014 ). Factors contributing to human reproduction and/or infertility identified in our review of involved genes include obesity, hormonal imbalance and protein-based disturbances such as leptin which is a key regulator of appetite produced by adipose tissue and known to inhibit ovarian steroidogenesis ( Moschos et al., 2002 ). This process influences sex hormone binding and androgen receptor sensitivity ( Peng et al., 2014 ) with increased levels of androgen resulting in apoptosis of granulosa cells with conversion of androgens peripherally to estrogens in fat cells. This inhibits gonadotrophin secretion and its level thereby impacting the hormone balance and fertility status of women with obesity ( Balen et al., 2006 ; Metwally et al., 2007 ; Fragouli et al., 2014 ; Bergh et al., 1993 ; Zaadstra et al., 1993 ). Obesity impacts fertility in women by also decreasing the conception rate with a relative risk for anovulatory infertility estimated at 2.7 ( Gesink Law et al., 2007 ; Wise et al., 2010 ; Rich-Edwards et al., 1994 ). Spontaneous conceptions are also known to decrease with subsequent increases in body mass index (BMI) in women. Obesity, therefore, impacts fertility and reproduction by overlapping shared genetic factors implicated or involved in perturbed metabolic and hormonal function ( Venkatesh et al., 2014 ). Infertility-related genes are noted to be involved with spermatogenesis (e.g .,ACVR2A,AR,ARNTL) , testes (e.g., ANKRD7, BAX, BCL2) or ovarian follicle development (e.g., AMH, BMP15, DMC1) , premature ovarian failure (e.g., FMR1) or primary ovarian insufficiency (e.g., SHOX, CCNH, HSD3B2 , GNAS), development of obesity or susceptibility (e.g., FTO, PCSK1, STAR) , gene expression or transcription activators (e.g., NFE2L3) or other transcription and translation factors (e.g., CRTC1, TCEB3B, NUPR1, EIF2B2) that are required for the proper development of somatotrophs, thyrotrophs and gonadotrophs ( PROP1 ), organization or function of the endoplasmic reticulum and protein export (e.g., SEC16B) or recycling (e.g., MAGEL2) , neuronal influences on body weight regulation (e.g., TMEM18) , testes-specific RNA splicing factors (e.g., TRA2B ) and transcription factors involved with genito-urinary or gonad development (e.g., WT1, CFTR) [genes reviewed in OMIM-( www.omim.org ) and Gene Cards ( www.genecards.org )]. Several obesity-related genes are clearly known to influence infertility by impacting hormonal status and related peptide production. Examples of obesity-related hormonal genes are LEP, LHB, AMH, INHA, GNRH1, IGF1, FSHB, FST, EPPIN, SHBG and IGF2 and examples of obesity-related peptide producing genes and receptors are AR, ESR1, INSR, FSHR, AMHR2, LHCGR, ACVR1, PPARG, STS, LEPR, VDR and IGF1R ( Butler et al., 2015 ). Thus, infertility susceptibility genes are known to affect common hormonal pathways along with related peptide production and their receptors, specifically those required for hormone storage and transport, gonadal structure and function and germ cell development, as noted in Table 1 . Advances in genetic technology using next generation sequencing of DNA exome or RNA expression data should allow for the discovery of hither to unknown disease-causing genes and their functional regulatory sequences, and thus enable a holistic understanding of commonly disturbed mechanisms in the development of human reproduction, ovulation, sperm production and infertility. This complete systems biological understanding has the potential to lead to targeted avenues of novel treatments and management in a significant number of infertile individuals. Therefore, molecular signatures of human reproduction and infertility-based gene profiles and coding expression patterns with overlap in interconnected disturbed gene pathways of infertility will be important to decipher and study. Further deciphering of infertility genomic perturbation and the resultant changes in the functional hormonal pathways will help characterize the disease mechanisms and processes to provide new targets for drug design and therapy. Characterization of these perturbations on an individual basis should not only lead to targeted more effective treatment modalities, but pave the way for prevention of infertility in the human population.

Our study involved a computer-based internet approach by searching peer-reviewed articles published in the medical literature [e.g., PubMed ( www.pubmed.org )] and other relevant computer-based authoritative websites including Online Mendelian Inheritance in Man ( www.OMIM.org ); GeneCards ( www.genecards.org ); and the National Center for Biotechnology Information. ( www.ncbi.nlm.nih.gov ). We searched keywords including human infertility, reproduction, meiosis, azoospermia, premature ovarian failure, primary ovarian insufficiency, endometriosis, diminished ovarian reserve and estrogen combined with other keywords such as genes, genetics, mutations or gene variants in order to identify sources with evidence for reproductive genetic factors that are supported by clinical, functional or experimental data for the causation of human infertility in both sexes. The title of the research articles found through this web-based search often contained the keywords of human infertility and genes (or genetics). The research articles were then examined for evidence of involvement of genes or genetic factors playing a role in human infertility or reproduction. Specifically, reviews of whole-genome-wide association studies (GWAS), gene linkage or expression patterns with DNA sequencing of infertile individuals identified a list of multiple genes which were compiled to develop an updated master list of such genes. We then plotted the recognized symbols for each gene that is known or is clinically relevant for causing human infertility and/or involved in reproduction onto high resolution (850 band level) chromosome ideograms ( Butler et al., 2015 ; Shaffer et al., 2013 ). The master list of all identified genes was then alphabetized by gene symbol, full name of the gene and chromosome band location in a tabular form. Genome-wide pathway analysis was carried out for the derived gene master list and all mapped genomic variants associated with human reproduction and related infertility using GeneAnalytics ( http://geneanalytics.genecards.org/ ), a commercially available software program based on proprietary, comprehensive and organized databases from the LifeMap suite. Mammalian genes were organized into functional categories based upon tissues and cells, diseases, pathways, GO-biological processes, GO-molecular function, phenotypes and compounds (endogenous or exogenous) with functional link to the queried gene set. Gene ontology (GO) terms (e.g., superpathways and GO-biological function) were scored based upon transformation of the binomial p-value which is equivalent to a corrected p-value with significance defined at p < 0.0001. Disease-matching scores were derived based upon the number of overlapping genes and the nature of the gene-disease association. Tissues and cells were scored using a matching algorithm that weighs tissue specificity, abundance and function of the gene. Related pathways were then grouped into superpathways to improve inferences, pathway enrichment, reduce redundancy, and rank genes within a biological mechanism via the multiplicity of constituent pathways ( Belinky et al., 2015 ).

We compiled an updated master list of clinically relevant genes for human reproduction and/or infertility by an extensive search of keywords related to human infertility, reproduction and genetics from peer-reviewed medical research articles and related nationally sponsored computer-based websites. The symbols for 371 genes were then plotted on high resolution human chromosome ideograms at precise chromosome band locations thereby producing a convenient visual image of the distribution of genetic factors contributing to human infertility and reproduction with alphabetical listing of genes in a tabular form allowing comparison to guide diagnosis, research, counseling and treatment particularly in individuals with chromosomal and/or genomic aberrations. The current number of genes identified in this report will vary in the future when stimulated by the latest advances in genomic technology and augmented by an increased number of subjects analyzed. The authors encourage the use of this current updated collection of clinically relevant candidate and known genes in the evaluation of patients and families in the clinical setting. This genetic information will in-turn encourage additional basic and translational research in human infertility and reproduction.

Infertility is the inability of couples who are sexually active and not taking contraceptives to achieve a pregnancy within one year. About 70 million infertile couples are noted worldwide and 10%–15% of the US population experiences infertility ( Silber and Barbey, 2012 ; Ombelet et al., 2008 ). Male infertility accounts for about 50% of infertile cases and can be multifactorial in origin; however, structural chromosomal and mitochondrial DNA abnormalities and hormonal/endocrine disturbances are also known. Non-genetic causes can include abnormal testicular development or descent, genital tract abnormalities, infection, age-related factors, chronic illnesses, impotence, medication and immunity status ( Shah et al., 2003 ). Female infertility is caused by hormonal, anatomical, genetic or environmental factors such as fibroids, tubal blockage, cervical mucus or chromosome abnormalities, pelvic inflammatory disease and age-related factors ( Olooto et al., 2012 ). Women beginning in their 30s will experience a greater than 25% chance of becoming infertile ( Silber and Barbey, 2012 ; Ombelet et al., 2008 ). An increased prevalence of human infertility and reproductive problems have been observed in westernized societies and is often related to a selected delay in establishing pregnancies by older women and the ensuing increase in genetic and hormonal imbalance with advancing age in both men and women. The increasing worldwide obesity epidemic further impacts reproduction by disturbing energy balance and expenditure often influenced by genetic and hormonal factors contributing to ovulation dysfunction, spontaneous abortions and overall infertility ( Silber and Barbey, 2012 ; Marsh and Hecker, 2014 ; Pandy et al., 2010 ; Balen et al., 2006 ; Gesink Law et al., 2007 ; Jungheim et al., 2012 ; Ogden et al., 2006 ). Genes encode proteins affecting reproductive organs and function, germ cell production and hormonal factors as well as those contributing to caloric intake (i.e., food seeking, eating behavior), body composition (fat and fat-free mass) and energy storage and utilization (physical activity and metabolism) ( Jungheim et al., 2012 ; Choquet and Meyre, 2011a , 2011b ; Zaadstra et al., 1993 ; Rich-Edwards et al., 1994 ; Metwally et al, 2007 ). Obesity often complicates reproduction by affecting genetic factors that are known to play a role in the coordination of many encoded proteins released at selected intervals for the establishment of pregnancies ( Jungheim er al., 2012 ; Metwally et al., 2007 ). For example, genetic-related conditions that correlate with decreased reproduction (e.g., fewer reproductive cycles) include women with polycystic ovarian syndrome (PCOS) and female carriers of the fragile X syndrome (i.e., FMR1 gene mutation) ( Pasquali and Gambineri, 2006 ; Peng et al., 2014 ; Ehrmann, 2005 ). About 5 to 10% of women from the general population are diagnosed with PCOS and over 40 genes are known to play a role in this disorder ( Venkatesh et al., 2014 ). A recent computer-based search of websites and peer-reviewed medical literature sources (e.g., www.pubmed.org ; www.ncbi.nlm.nih.gov ) using keywords related to obesity and genetics identified 370 clinically relevant candidate and known genes for obesity and similarly 153 human infertility and reproduction genes when searching keywords related to infertility and reproduction ( Butler et al., 2015 ). Among them, at least 21 genes were found to be associated with both obesity and human infertility. We now report an updated list of clinically relevant and known genes for human reproduction and related infertility with the display of gene symbols on high resolution (850 band level) chromosome ideograms and also alphabetically arranged in a tabular form. This illustrative effort of showing the location of genes involved with human infertility and reproduction on chromosome ideograms brings a better awareness of the gene(s) that might be involved in a given chromosomal aberration in an infertile couple and thereby render a more precise genetic basis for infertility, enabling a specific gene-based personalized medicine approach to treatment and genetic counseling. Additionally, GeneAnalytics ( http://geneanalytics.genecards.org/ ) was used to assess the underlying genetic architecture of human reproduction and related infertility by mapping the identified genes to tissues and cells, diseases, phenotypes, molecular pathways and biological processes with the greatest overlap and probable relevance.