Skip to main content Accessibility help
×
Hostname: page-component-55f67697df-xq6d9 Total loading time: 0 Render date: 2025-05-09T15:31:32.044Z Has data issue: false hasContentIssue false

Chapter 12 - Candidate Genes in Pregnancy Loss

Published online by Cambridge University Press:  16 April 2025

Roy G. Farquharson
Affiliation:
Liverpool Women’s Hospital
Mary D. Stephenson
Affiliation:
University of Illinois, Chicago
Mariëtte Goddijn
Affiliation:
Amsterdam University Medical Centers
Get access

Summary

This chapter will discuss the current state of miscarriage gene identification efforts using Chromosome Microarrays (CMA) and Next Generation Sequencing (NGS). CMA is an established clinical test for identifying genetic etiology of miscarriage with tens of thousands of cases reported. This allows finding hot-spots in the genome for copy number changes carrying candidate miscarriage genes as well as focusing on deeper analysis of individual genes within small CNVs. NGS studies for miscarriage candidate gene discovery and diagnosis are still relatively infrequent and include NGS of whole family, miscarriage only, couple only or women with recurrent pregnancy loss. Large scale integration of sequencing and CNV data in a pregnancy loss specific database, accompanied by obstetric and pathology findings is needed to facilitate identification of candidate genes and understanding of their role in adverse pregnancy outcome.

Type
Chapter
Information
Early Pregnancy , pp. 110 - 121
Publisher: Cambridge University Press
Print publication year: 2025

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

Book purchase

Temporarily unavailable

References

Yamada, H., Sata, F., Saijo, Y., Kishi, R., Minakami, H.. Genetic factors in fetal growth restriction and miscarriage. Semin Thromb Hemost. 2005;31(3):334–45.CrossRefGoogle ScholarPubMed
Christiansen, O. B., Steffensen, R., Nielsen, H. S., Varming, K.. Multifactorial etiology of recurrent miscarriage and its scientific and clinical implications. Gynecol Obstet Invest. 2008;66(4):257–67.CrossRefGoogle ScholarPubMed
Sierra, S., Stephenson, M.. Genetics of recurrent pregnancy loss. Semin Reprod Med. 2006;24(1):1724.CrossRefGoogle ScholarPubMed
Stephenson, M., Kutteh, W.. Evaluation and management of recurrent early pregnancy loss. Clin Obstet Gynecol. 2007;50(1):132–45.CrossRefGoogle ScholarPubMed
Rajcan-Separovic, E.. Chromosome microarrays in human reproduction. Hum Reprod Update. 2012;18(5):555–67.CrossRefGoogle ScholarPubMed
Schaaf, C. P., Wiszniewska, J., Beaudet, A. L.. Copy number and SNP arrays in clinical diagnostics. Annu Rev Genomics Hum Genet. 2011;12:2551.CrossRefGoogle ScholarPubMed
Riggs, E. R., Andersen, E. F., Cherry, A. M., Kantarci, S., Kearney, H., Patel, A., et al. Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen). Genet Med. 2020;22(2):245–57.CrossRefGoogle ScholarPubMed
Committee on Genetics and the Society for Maternal–Fetal Medicine. Committee opinion no. 682 summary: microarrays and next-generation sequencing technology: the use of advanced genetic diagnostic tools in obstetrics and gynecology. Obstet Gynecol. 2016;128(6):1462–63.Google Scholar
Finley, J., Hay, S., Oldzej, J., Meredith, M. M., Dzidic, N., Slim, R., et al. The genomic basis of sporadic and recurrent pregnancy loss: a comprehensive in-depth analysis of 24,900 miscarriages. Reprod Biomed Online. 2022;45(1):125–34.CrossRefGoogle Scholar
Peng, G., Zhou, Q., Chai, H., Wen, J., Zhao, H., Taylor, H. S., et al. Estimation on risk of spontaneous abortions by genomic disorders from a meta-analysis of microarray results on large case series of pregnancy losses. Mol Genet Genomic Med. 2023;11(8):e2181.CrossRefGoogle ScholarPubMed
Colley, E., Hamilton, S., Smith, P., Morgan, N. V., Coomarasamy, A., Allen, S.. Potential genetic causes of miscarriage in euploid pregnancies: a systematic review. Hum Reprod Update. 2019;25(4):452–72.CrossRefGoogle ScholarPubMed
Wang, Y., Li, Y., Chen, Y., Zhou, R., Sang, Z., Meng, L., et al. Systematic analysis of copy-number variations associated with early pregnancy loss. Ultrasound Obstet Gynecol. 2020;55(1):96104.CrossRefGoogle ScholarPubMed
Pauta, M., Grande, M., Rodriguez-Revenga, L., Kolomietz, E., Borrell, A.. Added value of chromosomal microarray analysis over karyotyping in early pregnancy loss: systematic review and meta-analysis. Ultrasound Obstet Gynecol. 2018;51(4):453–62.CrossRefGoogle ScholarPubMed
Rajcan-Separovic, E., Qiao, Y., Tyson, C., Harvard, C., Fawcett, C., Kalousek, D., et al. Genomic changes detected by array CGH in human embryos with developmental defects. Mol Hum Reprod. 2010;16(2):125–34.CrossRefGoogle Scholar
Reis, L. M., Sorokina, E. A., Thompson, S., Muheisen, S., Velinov, M., Zamora, C., et al. De novo missense variants in WDR37 cause a severe multisystemic syndrome. Am J Hum Genet. 2019;105(2):425–33.CrossRefGoogle Scholar
Ta-Shma, A., Perles, Z., Yaacov, B., Werner, M., Frumkin, A., Rein, A. J., et al. A human laterality disorder associated with a homozygous WDR16 deletion. Eur J Hum Genet. 2015;23(9):1262–65.CrossRefGoogle ScholarPubMed
Rajcan-Separovic, E., Diego-Alvarez, D., Robinson, W. P., Tyson, C., Qiao, Y., Harvard, C., et al. Identification of copy number variants in miscarriages from couples with idiopathic recurrent pregnancy loss. Hum Reprod. 2010;25(11):2913–22.CrossRefGoogle ScholarPubMed
Wen, J., Hanna, C. W., Martell, S., Leung, P. C., Lewis, S.M., Robinson, W.P., et al. Functional consequences of copy number variants in miscarriage. Mol Cytogenet. 2015;8:6.CrossRefGoogle ScholarPubMed
Okamoto, T., Niu, R., Yamada, S., Osawa, M.. Reduced expression of tissue inhibitor of metalloproteinase (TIMP)-2 in gestational trophoblastic diseases. Mol Hum Reprod. 2002;8(4):392–98.CrossRefGoogle ScholarPubMed
Kline, J., Vardarajan, B., Abhyankar, A., Kytömaa, S., Levin, B., Sobreira, N., et al. Embryonic lethal genetic variants and chromosomally normal pregnancy loss. Fertil Steril. 2021;116(5):1351–58.CrossRefGoogle ScholarPubMed
Du, Q., de la Morena, M. T., van Oers, N. S. C.. The genetics and epigenetics of 22q11.2 deletion syndrome. Front Genet. 2019;10:1365.CrossRefGoogle ScholarPubMed
Chen, Y., Bartanus, J., Liang, D., Zhu, H., Breman, A. M., Smith, J. L., et al. Characterization of chromosomal abnormalities in pregnancy losses reveals critical genes and loci for human early development. Hum Mutat. 2017;38(6):669–77.CrossRefGoogle ScholarPubMed
Bagheri, H., Mercier, E., Qiao, Y., Stephenson, M. D., Rajcan-Separovic, E.. Genomic characteristics of miscarriage copy number variants. Mol Hum Reprod. 2015;21(8):655–61.CrossRefGoogle ScholarPubMed
Nagirnaja, L., Palta, P., Kasak, L., Rull, K., Christiansen, O. B., Nielsen, H. S., et al. Structural genomic variation as risk factor for idiopathic recurrent miscarriage. Hum Mutat. 2014;35(8):972–82.CrossRefGoogle ScholarPubMed
Zhu, S., Lin, D., Ye, Z., Chen, X., Jiang, W., Xu, H., et al. GOLPH3 modulates expression and alternative splicing of transcription factors associated with endometrial decidualization in human endometrial stromal cells. PeerJ. 2023;11:e15048.CrossRefGoogle ScholarPubMed
Migita, O., Maehara, K., Kamura, H., Miyakoshi, K., Tanaka, M., Morokuma, S., et al. Compilation of copy number variants identified in phenotypically normal and parous Japanese women. J Hum Genet. 2014;59(6):326–31.CrossRefGoogle ScholarPubMed
Bamshad, M. J., Ng, S. B., Bigham, A. W., Tabor, H. K., Emond, M. J., Nickerson, D. A., et al. Exome sequencing as a tool for Mendelian disease gene discovery. Nat Rev Genet. 2011;12(11):745–55.CrossRefGoogle ScholarPubMed
Gilissen, C., Hoischen, A., Brunner, H. G., Veltman, J. A.. Disease gene identification strategies for exome sequencing. Eur J Hum Genet. 2012;20(5):490–97.CrossRefGoogle ScholarPubMed
Vora, N. L., Hui, L.. Next-generation sequencing and prenatal ‘omics: advanced diagnostics and new insights into human development. Genet Med. 2018;20(8):791–99.CrossRefGoogle ScholarPubMed
Richards, S., Aziz, N., Bale, S., Bick, D., Das, S., Gastier-Foster, J., et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17(5):405–24.CrossRefGoogle ScholarPubMed
Chau, M. H. K, Choy, K. W.. The role of chromosomal microarray and exome sequencing in prenatal diagnosis. Curr Opin Obstet Gynecol. 2021;33(2):148–55.CrossRefGoogle ScholarPubMed
Monaghan, K. G., Leach, N. T., Pekarek, D., Prasad, P., Rose, N. C., ACMG Professional Practice and Guidelines Committee. The use of fetal exome sequencing in prenatal diagnosis: a points to consider document of the American College of Medical Genetics and Genomics (ACMG). Genet Med. 2020;22(4):675–80.CrossRefGoogle ScholarPubMed
Mellis, R., Oprych, K., Scotchman, E., Hill, M., Chitty, L. S.. Diagnostic yield of exome sequencing for prenatal diagnosis of fetal structural anomalies: a systematic review and meta-analysis. Prenat Diagn. 2022;42(6):662–85.CrossRefGoogle ScholarPubMed
Rajcan-Separovic, E.. Next generation sequencing in recurrent pregnancy loss – approaches and outcomes. Eur J Med Genet. 2020;63(2):103644.CrossRefGoogle ScholarPubMed
Robbins, S. M., Thimm, M. A., Valle, D., Jelin, A. C.. Genetic diagnosis in first or second trimester pregnancy loss using exome sequencing: a systematic review of human essential genes. J Assist Reprod Genet. 2019;36(8):1539–48.CrossRefGoogle ScholarPubMed
Byrne, A. B., Arts, P., Ha, T. T., Kassahn, K. S., Pais, L. S., O’Donnell-Luria, A., et al. Genomic autopsy to identify underlying causes of pregnancy loss and perinatal death. Nat Med. 2023;29(1):180–89.CrossRefGoogle ScholarPubMed
Chen, X., Jiang, Y., Chen, R., Qi, Q., Zhang, X., Zhao, S., et al. Clinical efficiency of simultaneous CNV-seq and whole-exome sequencing for testing fetal structural anomalies. J Transl Med. 2022;20(1):10.CrossRefGoogle ScholarPubMed
Najafi, K., Mehrjoo, Z., Ardalani, F., Ghaderi-Sohi, S., Kariminejad, A., Kariminejad, R., et al. Identifying the causes of recurrent pregnancy loss in consanguineous couples using whole exome sequencing on the products of miscarriage with no chromosomal abnormalities. Sci Rep. 2021;11(1):6952.CrossRefGoogle ScholarPubMed
Filges, I., Nosova, E., Bruder, E., Tercanli, S., Townsend, K., Gibson, W. T., et al. Exome sequencing identifies mutations in KIF14 as a novel cause of an autosomal recessive lethal fetal ciliopathy phenotype. Clin Genet. 2014;86(3):220–28.CrossRefGoogle ScholarPubMed
Reilly, M. L., Stokman, M. F., Magry, V., Jeanpierre, C., Alves, M., Paydar, M., et al. Loss-of-function mutations in KIF14 cause severe microcephaly and kidney development defects in humans and zebrafish. Hum Mol Genet. 2019;28(5):778–95.CrossRefGoogle ScholarPubMed
Cristofoli, F., De Keersmaecker, B., De Catte, L., Vermeesch, J. R., Van Esch, H.. Novel STIL compound heterozygous mutations cause severe fetal microcephaly and centriolar lengthening. Mol Syndromol. 2017;8(6):282–93.CrossRefGoogle ScholarPubMed
Spellicy, C. J., Norris, J., Bend, R., Bupp, C., Mester, P., Reynolds, T., et al. Key apoptotic genes APAF1 and CASP9 implicated in recurrent folate-resistant neural tube defects. Eur J Hum Genet. 2018;26(3):420–27.CrossRefGoogle ScholarPubMed
Wang, X., Shi, W., Zhao, S., Gong, D., Li, S., Hu, C., et al. Whole exome sequencing in unexplained recurrent miscarriage families identified novel pathogenic genetic causes of euploid miscarriage. Hum Reprod. 2023;38(5):1003–18.CrossRefGoogle ScholarPubMed
Qiao, Y., Wen, J., Tang, F., Martell, S., Shomer, N., Leung, P. C. K., et al. Whole exome sequencing in recurrent early pregnancy loss. Mol Hum Reprod. 2016;22(5):364–72.CrossRefGoogle ScholarPubMed
Dagoneau, N., Goulet, M., Geneviève, D., Sznajer, Y., Martinovic, J., Smithson, S., et al. DYNC2H1 mutations cause asphyxiating thoracic dystrophy and short rib-polydactyly syndrome, type III. Am J Hum Genet. 2009;84(5):706–11.CrossRefGoogle ScholarPubMed
Singh, N. K., Rao, G. N.. Emerging role of 12/15-lipoxygenase (ALOX15) in human pathologies. Prog Lipid Res. 2019;73:2845.CrossRefGoogle ScholarPubMed
Shamseldin, H. E., Tulbah, M., Kurdi, W., Nemer, M., Alsahan, N., Al Mardawi, E., et al. Identification of embryonic lethal genes in humans by autozygosity mapping and exome sequencing in consanguineous families. Genome Biol. 2015;16(1):116.CrossRefGoogle ScholarPubMed
Shamseldin, H. E., Kurdi, W., Almusafri, F., Alnemer, M., Alkaff, A., Babay, Z., et al. Molecular autopsy in maternal-fetal medicine. Genet Med. 2018;20(4):420–27.CrossRefGoogle ScholarPubMed
Zhao, C., Chai, H., Zhou, Q., Wen, J., Reddy, U. M., Kastury, R., et al. Exome sequencing analysis on products of conception: a cohort study to evaluate clinical utility and genetic etiology for pregnancy loss. Genet Med. 2021;23(3):435–42.CrossRefGoogle Scholar
Buonaiuto, S., Biase, I. D., Aleotti, V., Ravaei, A., Marino, A., Damaggio, G., et al. Prioritization of putatively detrimental variants in euploid miscarriages. Sci Rep. 2022;12(1):1997.CrossRefGoogle ScholarPubMed
Dong, Z., Yan, J., Xu, F., Yuan, J., Jiang, H., Wang, H., et al. Genome sequencing explores complexity of chromosomal abnormalities in recurrent miscarriage. Am J Hum Genet. 2019;105(6):1102–11.CrossRefGoogle ScholarPubMed
Stals, K. L., Wakeling, M., Baptista, J., Caswell, R., Parrish, A., Rankin, J., et al. Diagnosis of lethal or prenatal-onset autosomal recessive disorders by parental exome sequencing. Prenat Diagn. 2018;38(1):3343.CrossRefGoogle ScholarPubMed
Ellard, S., Kivuva, E., Turnpenny, P., Stals, K., Johnson, M., Xie, W., et al. An exome sequencing strategy to diagnose lethal autosomal recessive disorders. Eur J Hum Genet. 2015;23(3):401–4.CrossRefGoogle ScholarPubMed
Aminbeidokhti, M., Qu, J.-H., Belur, S., Cakmak, H., Jaswa, E., Lathi, R. B., et al. Preconception genetic carrier screening for miscarriage risk assessment: a bioinformatic approach to identifying candidate lethal genes and variants. medRxiv. 2023.CrossRefGoogle Scholar
Filges, I., Manokhina, I., Peñaherrera, M. S., McFadden, D. E., Louie, K., Nosova, E., et al. Recurrent triploidy due to a failure to complete maternal meiosis II: whole-exome sequencing reveals candidate variants. Mol Hum Reprod. 2015;21(4):339–46.CrossRefGoogle ScholarPubMed
Quintero-Ronderos, P., Mercier, E., Fukuda, M., González, R., Suárez, C. F., Patarroyo, M. A., et al. Novel genes and mutations in patients affected by recurrent pregnancy loss. PLoS One. 2017;12(10):e0186149.CrossRefGoogle ScholarPubMed
Xiang, H., Wang, C., Pan, H., Hu, Q., Wang, R., Xu, Z., et al. Exome-sequencing identifies novel genes associated with recurrent pregnancy loss in a Chinese cohort. Front Genet. 2021;12:746082.CrossRefGoogle Scholar
Maddirevula, S., Awartani, K., Coskun, S., AlNaim, L. F., Ibrahim, N., Abdulwahab, F., et al. A genomics approach to females with infertility and recurrent pregnancy loss. Hum Genet. 2020;139(5):605–13.CrossRefGoogle ScholarPubMed

Save book to Kindle

To save this book to your Kindle, first ensure [email protected] is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about saving to your Kindle.

Note you can select to save to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be saved to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

Find out more about the Kindle Personal Document Service.

Available formats
×

Save book to Dropbox

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Dropbox.

Available formats
×

Save book to Google Drive

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Google Drive.

Available formats
×