Browsing by Subject "WGS"

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    Multiple molecular diagnoses identified through genome sequencing in individuals with suspected rare disease
    (Elsevier, 2025-04-07) Malhotra, Alka; Thorpe, Erin; Coffey, Alison J.; Rajkumar, Revathi; Adjeman, Josephine; Adjeley Adjetey, Naomi Dianne Naa; Aglobitse, Sharron; Allotey, Felix; Arsov, Todor; Ashong, Joyce; Badoe, Ebenezer Vincent; Basel, Donald; Brew, Yvonne; Brown, Chester; Bosfield, Kerri; Casas, Kari; Cornejo-Olivas, Mario; Davis-Keppen, Laura; Freed, Abbey; Gibson, Kate; Jayakar, Parul; Jones, Marilyn C.; Kawome, Martina; Lumaka, Aimé; Maier, Ursula; Makay, Prince; Manassero, Gioconda; Marbell-Wilson, Marilyn; Marcuccilli, Charles; Masser-Frye, Diane; McCarrier, Julie; Mills, Hannah-Sharon; Balazar Montoya, Jeny; Mubungu, Gerrye; Ngole, Mamy; Perez, Jorge; Pivnick, Eniko; Duenas-Roque, Milagros M.; Salguero, Hildegard Pena; Serize, Arturo; Shinawi, Marwan; Sirchia, Fabio; Soler-Alfonso, Claudia; Taylor, Alan; Thompson, Lauren; Vance, Gail; Vanderver, Adeline; Vaux, Keith; Velasco, Danita; Wiafe, Samuel; Illumina Laboratory Services Interpretation and Reporting Team; Taft, Ryan J.; Perry, Denise L.; Kesari, Akanchha; Medical and Molecular Genetics, School of Medicine
    Genome sequencing is a powerful and comprehensive test that detects multiple variants of different types. The interrogation of variants across the genome enables the identification of multiple molecular diagnoses (MMDs) in a single individual. In this retrospective study, we describe individuals in whom MMDs were associated with the proband's indication for testing (IFT), secondary findings, or incidental findings. An MMD is considered where at least one of the findings is associated with the primary IFT and all variants are classified as either likely pathogenic or pathogenic. Clinical genome sequencing was performed for all individuals as part of the iHope program at the Illumina Laboratory Services between September 2017 and December 2023. The iHope cohort included 1,846 affected individuals, with 872 (47.2%) found to have at least one likely pathogenic or pathogenic variant associated with the primary IFT. Of these, 81 (9.3%) individuals had multiple clinically significant molecular findings, including 76 individuals with reported variants associated with 2 different conditions, and 5 individuals with more than 2 molecular findings. A total of 32 individuals (3.7%) had at least 2 molecular diagnoses related to the primary IFT, while in 49 (5.6%) individuals, the variant(s) reported for the second condition constituted a secondary or incidental finding. Our study highlights that among individuals with a likely pathogenic or pathogenic finding identified through genome sequencing, 9% have MMDs, which may have been missed with different testing methods. Of note, approximately 60% of the 81 individuals with an MMD had a potentially actionable secondary or incidental finding.
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    Read-depth based approach on whole genome resequencing data reveals important insights into the copy number variation (CNV) map of major global buffalo breeds
    (BMC, 2023-10-16) Ahmad, Sheikh Firdous; Shailaja, Celus Chandrababu; Vaishnav, Sakshi; Kumar, Amit; Gaur, Gyanendra Kumar; Janga, Sarath Chandra; Ahmad, Syed Mudasir; Malla, Waseem Akram; Dutt, Triveni; Medical and Molecular Genetics, School of Medicine
    Background: Elucidating genome-wide structural variants including copy number variations (CNVs) have gained increased significance in recent times owing to their contribution to genetic diversity and association with important pathophysiological states. The present study aimed to elucidate the high-resolution CNV map of six different global buffalo breeds using whole genome resequencing data at two coverages (10X and 30X). Post-quality control, the sequence reads were aligned to the latest draft release of the Bubaline genome. The genome-wide CNVs were elucidated using a read-depth approach in CNVnator with different bin sizes. Adjacent CNVs were concatenated into copy number variation regions (CNVRs) in different breeds and their genomic coverage was elucidated. Results: Overall, the average size of CNVR was lower at 30X coverage, providing finer details. Most of the CNVRs were either deletion or duplication type while the occurrence of mixed events was lesser in number on a comparative basis in all breeds. The average CNVR size was lower at 30X coverage (0.201 Mb) as compared to 10X (0.013 Mb) with the finest variants in Banni buffaloes. The maximum number of CNVs was observed in Murrah (2627) and Pandharpuri (25,688) at 10X and 30X coverages, respectively. Whereas the minimum number of CNVs were scored in Surti at both coverages (2092 and 17,373). On the other hand, the highest and lowest number of CNVRs were scored in Jaffarabadi (833 and 10,179 events) and Surti (783 and 7553 events) at both coverages. Deletion events overnumbered duplications in all breeds at both coverages. Gene profiling of common overlapped genes and longest CNVRs provided important insights into the evolutionary history of these breeds and indicate the genomic regions under selection in respective breeds. Conclusion: The present study is the first of its kind to elucidate the high-resolution CNV map in major buffalo populations using a read-depth approach on whole genome resequencing data. The results revealed important insights into the divergence of major global buffalo breeds along the evolutionary timescale.