Absence of heterozygosity (AOH) is a genetic characteristic known to cause human genetic disorders through autosomal recessive or imprinting mechanisms. However, the analysis of AOH via low-pass genome sequencing (GS) is not yet clinically available.
Low-pass GS (fourfold) with different types of libraries was performed on 17 clinical samples with previously ascertained AOH by chromosomal microarray analysis (CMA). In addition, AOH detection was performed with low-pass GS data in 1,639 cases that had both GS and high-probe density CMA data available from the 1000 Genomes Project. Cases with multiple AOHs (coefficient of inbreeding F ≥ 1/32) or terminal AOHs ≥5 Mb (suspected uniparental disomy [UPD]) were reported based on the guidelines of the American College of Medical Genetics and Genomics.
Low-pass GS revealed suspected segmental UPD and multiple AOHs (F ≥ 1/32) in nine and eight clinical cases, respectively, consistent with CMA. Among the 1,639 samples, low-pass GS not only consistently detected multiple AOHs (F ≥ 1/32) in 18 cases, but also reported 60 terminal AOHs in 44 cases including four mosaic AOHs at a level ranging from 50% to 75%.
Overall, our study demonstrates the feasibility of AOH analysis (≥5 Mb) with low-pass GS data and shows high concordance compared with CMA.
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Genome sequencing data used in this study have been made available in the CNGB Nucleotide Sequence Archive (CNSA: https://db.cngb.org/cnsa/) under the accession number CNP0000558.
All programs relevant to this pipeline are available at https://sourceforge.net/projects/lpgsaoh/files/.
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This project is supported by the National Natural Science Foundation of China (31801042), the Health and Medical Research Fund (04152666, 07180576), 2018 Shenzhen Virtue University Park Laboratory Support Special Fund (YFJGJS1.0) for Key Laboratory for Regenerative Medicine, Ministry of Education (Shenzhen Base), General Research Fund (14115418), and Direct Grant (2019.051). C.C.M. is supported by NIH/NIGMS P01 GM0613S4 and the NIHR Manchester Biomedical Research Centre, UK. We thank the 1000 Genomes Project for releasing the GS and CMA data. The following cell lines/DNA samples were obtained from the NIGMS Human Genetic Cell Repository at the Coriell Institute for Medical Research: [NA06984, NA06985, NA06986, NA06989, NA06994, NA07000, NA07037, NA07048, NA07051, NA07056, NA07347, NA07357, NA10847, NA10851, NA11829, NA11830, NA11831, NA11832, NA11840, NA11843, NA11881, NA11892, NA11893, NA11894, NA11918, NA11919, NA11920, NA11930. NA11931, NA11932, NA11933, NA11992, NA11994, NA11995, NA12003, NA12004, NA12005, NA12006, NA12043, NA12044, NA12045, NA12046, NA12058, NA12144, NA12154, NA12155, NA12156, NA12234, NA12249, NA12272, NA12273, NA12275, NA12282, NA12283, NA12286, NA12287, NA12340, NA12341, NA12342, NA12347, NA12348, NA12383, NA12399, NA12400, NA12413,, NA12414, NA12489, NA12546, NA12716, NA12717, NA12718, NA12748, NA12749, NA12750, NA12751, NA12760, NA12761, NA12762, NA12763, NA12775, NA12776, NA12777, NA12778, NA12812, NA12813, NA12814, NA12815, NA12827, NA12828, NA12829, NA12830, NA12842, NA12843, NA12872, NA12873, NA12874, NA12878, NA12889, NA12890]. These genome sequencing data were generated at the New York Genome Center with funds provided by NHGRI Grant 3UM1HG008901-03S1.
The study protocol was approved by the Ethics Committee of the Joint Chinese University of Hong Kong–New Territories East Cluster Clinical Research Ethics Committee (CREC reference number 2016.713). Written consent for sample storage and genetic analyses was obtained from each participant.
The authors declare no competing interests.
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Dong, Z., Chau, M.H.K., Zhang, Y. et al. Low-pass genome sequencing–based detection of absence of heterozygosity: validation in clinical cytogenetics. Genet Med (2021). https://doi.org/10.1038/s41436-021-01128-7