Diagnostic exome-based preconception carrier testing in consanguineous couples: results from the first 100 couples in clinical practice

• Published in: Genetics in medicine Vol. 23; no. 6; pp. 1125 - 1136
• Main Authors: Sallevelt, Suzanne C.E.H., Stegmann, Alexander P.A., de Koning, Bart, Velter, Crool, Steyls, Anja, van Esch, Melanie, Lakeman, Phillis, Yntema, Helger, Esteki, Masoud Zamani, de Die-Smulders, Christine E.M., Gilissen, Christian, van den Wijngaard, Arthur, Brunner, Han G., Paulussen, Aimée D.C.
• Format: Journal Article
• Language: English
• Published: New York Elsevier Inc 01.06.2021; Nature Publishing Group US; Elsevier Limited
• Subjects: Biomedical and Life Sciences; Biomedicine; Clinical medicine; Congenital diseases; Consanguinity; Couples; Exome - genetics; Family; Family medical history; Genes; Genetic counseling; Genetic engineering; Genomics; Health risk assessment; Heterozygote; Human Genetics; Laboratories; Laboratory Medicine; Neurosciences; Whole Exome Sequencing
• ISSN: 1098-3600; 1530-0366
• DOI: 10.1038/s41436-021-01116-x

Consanguineous couples are at increased risk of being heterozygous for the same autosomal recessive (AR) disorder(s), with a 25% risk of affected offspring as a consequence. Until recently, comprehensive preconception carrier testing (PCT) for AR disorders was unavailable in routine diagnostics. Here we developed and implemented such a test in routine clinical care. We performed exome sequencing (ES) for 100 consanguineous couples. For each couple, rare variants that could give rise to biallelic variants in offspring were selected. These variants were subsequently filtered against a gene panel consisting of ~2,000 genes associated with known AR disorders (OMIM-based). Remaining variants were classified according to American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines, after which only likely pathogenic and pathogenic (class IV/V) variants, present in both partners, were reported. In 28 of 100 tested consanguineous couples (28%), likely pathogenic and pathogenic variants not previously known in the couple or their family were reported conferring 25% risk of affected offspring. ES-based PCT provides a powerful diagnostic tool to identify AR disease carrier status in consanguineous couples. Outcomes provided significant reproductive choices for a higher proportion of these couples than previous tests.