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Annotated VCF Files for WGS of ASD Cohort with 68 Individuals from 22 families, enriched for recent shared ancestry

We performed whole genome sequencing (WGS) in an ASD cohort of 68 individuals from 22 families enriched for recent shared ancestry. Samples were sequenced using Illumina HiSeq X platform, and Variants (single nucleotide variants (SNVs) and insertions or deletions (indels)) were detected using GATK with HaplotypeCaller. Quality control checks for (i) duplicate samples, (ii) samples per platform, (iii) genome call rate, (iv) missingness rate, (v) singleton rate, (vi) heterozygosity rate, (vii) homozygosity rate, (viii) Ti/Tv ratio, (ix) inbreeding coefficient, and (x) sex inference were performed as previously described. Variant call format (VCF) files for SNVs and indels were annotated with ANNOVAR using allele frequencies from the 1000 Genomes project (2015; 1000G), the Genome Aggregation Database (gnomAD), and the Greater Middle East Variome Project (GME).

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This agreement governs the terms on which access will be granted to the whole genome sequence data generated and published in this study: Analysis of recent shared ancestry in a familial cohort identifies coding and noncoding autism spectrum disorder variants, Tuncay et al., npj Genomic Medicine, 2022. In signing this agreement, you are agreeing to be bound by the terms and conditions of access set out in this agreement. For the sake of clarity, the terms of access set out in this agreement apply both to the User and the User’s Institution (as defined below). User Institution and User are referred to within the agreement as “you” and “your” shall be construed accordingly.

Definitions: Data means all and any human genetic data obtained under this Database Access Agreement. Data Subject means a person, who has been informed of the purpose for which the Data is held and has given his/her informed consent thereto. User means a researcher whose User Institution has previously completed this Data Access Agreement and has received acknowledgement of its acceptance. Publications means, without limitation, articles published in print journals, electronic journals, reviews, books, posters, and other written and verbal presentations of research performed using the Data. User Institution means the organization at which the User is employed, affiliated with, or enrolled. Terms and Conditions: In signing this Agreement: 1. You agree to use the Data only for the advancement of medical research in accordance with the approved proposal that you submitted unless otherwise required by law. 2. 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The University of Texas Southwestern Medical Center agrees to treat the report and all information, data, results, and conclusions contained within such a report as confidential information belonging to the User Institution. 16. You accept that the Data are protected by and subject to laws in various international jurisdictions, including without limitation laws in the USA, EAA, and Canada, and that you are responsible for ensuring compliance with any such applicable law. The Data Access Committee reserves the right to request and inspect data security and management documentation to ensure the adequacy of data protection measures in countries that have no national laws comparable to that which pertain in the USA, EAA, and Canada. 17. 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Authors who use data from the project must include an acknowledgement using the following wording "This study makes use of data generated by the laboratory of Dr. Maria Chahrour at the University of Texas Southwestern Medical Center and by the Autism Speaks MSSNG Project, including The Hospital for Sick Children (Toronto)." and cite the relevant publication: Analysis of recent shared ancestry in a familial cohort identifies coding and noncoding autism spectrum disorder variants, Tuncay et al., npj Genomic Medicine, 2022. Users should note that the University of Texas Southwestern Medical Center and The Hospital for Sick Children bear no responsibility for the further analysis or interpretation of these data, over and above that published by the University of Texas Southwestern Medical Center and/or The Hospital for Sick Children. 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Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
EGAS00001006058 Other

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Located in
EGAF00005858407 vcf.gz 219.8 MB
EGAF00005858408 vcf.gz 219.1 MB
EGAF00005858409 vcf.gz 223.1 MB
EGAF00005858410 vcf.gz 220.4 MB
EGAF00005858411 vcf.gz 219.7 MB
EGAF00005858412 vcf.gz 215.2 MB
EGAF00005858413 vcf.gz 210.7 MB
EGAF00005858414 vcf.gz 215.4 MB
EGAF00005858415 vcf.gz 218.5 MB
EGAF00005858416 vcf.gz 217.8 MB
EGAF00005858417 vcf.gz 213.3 MB
EGAF00005858418 vcf.gz 221.0 MB
EGAF00005858419 vcf.gz 213.7 MB
EGAF00005858420 vcf.gz 216.4 MB
EGAF00005858421 vcf.gz 224.1 MB
EGAF00005858422 vcf.gz 221.8 MB
EGAF00005858423 vcf.gz 216.1 MB
EGAF00005858424 vcf.gz 215.5 MB
EGAF00005858425 vcf.gz 212.4 MB
EGAF00005858426 vcf.gz 217.2 MB
EGAF00005858427 vcf.gz 215.8 MB
EGAF00005858428 vcf.gz 222.0 MB
EGAF00005858429 vcf.gz 215.1 MB
EGAF00005858430 vcf.gz 221.3 MB
EGAF00005858431 vcf.gz 216.6 MB
EGAF00005858432 vcf.gz 218.0 MB
EGAF00005858433 vcf.gz 221.6 MB
EGAF00005858434 vcf.gz 217.9 MB
EGAF00005858435 vcf.gz 206.4 MB
EGAF00005858436 vcf.gz 209.7 MB
EGAF00005858437 vcf.gz 215.2 MB
EGAF00005858438 vcf.gz 214.9 MB
EGAF00005858439 vcf.gz 216.2 MB
EGAF00005858440 vcf.gz 221.2 MB
EGAF00005858441 vcf.gz 219.7 MB
EGAF00005858442 vcf.gz 214.6 MB
EGAF00005858443 vcf.gz 221.4 MB
EGAF00005858444 vcf.gz 221.1 MB
EGAF00005858445 vcf.gz 216.1 MB
EGAF00005858446 vcf.gz 210.3 MB
EGAF00005858447 vcf.gz 215.4 MB
EGAF00005858448 vcf.gz 221.3 MB
EGAF00005858449 vcf.gz 208.6 MB
EGAF00005858450 vcf.gz 205.9 MB
EGAF00005858451 vcf.gz 211.8 MB
EGAF00005858452 vcf.gz 205.9 MB
EGAF00005858453 vcf.gz 211.6 MB
EGAF00005858454 vcf.gz 213.6 MB
EGAF00005858455 vcf.gz 223.0 MB
EGAF00005858456 vcf.gz 211.4 MB
EGAF00005858457 vcf.gz 216.5 MB
EGAF00005858458 vcf.gz 204.8 MB
EGAF00005858459 vcf.gz 211.6 MB
EGAF00005858460 vcf.gz 216.7 MB
EGAF00005858461 vcf.gz 210.7 MB
EGAF00005858462 vcf.gz 215.5 MB
EGAF00005858463 vcf.gz 217.6 MB
EGAF00005858464 vcf.gz 214.9 MB
EGAF00005858465 vcf.gz 212.7 MB
EGAF00005858466 vcf.gz 214.2 MB
EGAF00005858467 vcf.gz 211.9 MB
EGAF00005858468 vcf.gz 200.4 MB
EGAF00005858469 vcf.gz 223.7 MB
EGAF00005858470 vcf.gz 205.0 MB
EGAF00005858471 vcf.gz 212.7 MB
EGAF00005858472 vcf.gz 210.2 MB
EGAF00005858473 vcf.gz 210.6 MB
EGAF00005858474 vcf.gz 210.6 MB
EGAF00005858475 tbi 1.6 MB
EGAF00005858476 tbi 1.7 MB
EGAF00005858477 tbi 1.6 MB
EGAF00005858478 tbi 1.6 MB
EGAF00005858479 tbi 1.7 MB
EGAF00005858480 tbi 1.7 MB
EGAF00005858481 tbi 1.6 MB
EGAF00005858482 tbi 1.6 MB
EGAF00005858483 tbi 1.7 MB
EGAF00005858484 tbi 1.7 MB
EGAF00005858485 tbi 1.7 MB
EGAF00005858486 tbi 1.6 MB
EGAF00005858487 tbi 1.6 MB
EGAF00005858488 tbi 1.6 MB
EGAF00005858489 tbi 1.7 MB
EGAF00005858490 tbi 1.7 MB
EGAF00005858491 tbi 1.7 MB
EGAF00005858492 tbi 1.6 MB
EGAF00005858493 tbi 1.7 MB
EGAF00005858494 tbi 1.6 MB
EGAF00005858495 tbi 1.7 MB
EGAF00005858496 tbi 1.6 MB
EGAF00005858497 tbi 1.6 MB
EGAF00005858498 tbi 1.7 MB
EGAF00005858499 tbi 1.6 MB
EGAF00005858500 tbi 1.6 MB
EGAF00005858501 tbi 1.7 MB
EGAF00005858502 tbi 1.7 MB
EGAF00005858503 tbi 1.7 MB
EGAF00005858504 tbi 1.6 MB
EGAF00005858505 tbi 1.6 MB
EGAF00005858506 tbi 1.7 MB
EGAF00005858507 tbi 1.6 MB
EGAF00005858508 tbi 1.6 MB
EGAF00005858509 tbi 1.7 MB
EGAF00005858510 tbi 1.6 MB
EGAF00005858511 tbi 1.6 MB
EGAF00005858512 tbi 1.6 MB
EGAF00005858513 tbi 1.7 MB
EGAF00005858514 tbi 1.7 MB
EGAF00005858515 tbi 1.7 MB
EGAF00005858516 tbi 1.7 MB
EGAF00005858517 tbi 1.7 MB
EGAF00005858518 tbi 1.7 MB
EGAF00005858519 tbi 1.7 MB
EGAF00005858520 tbi 1.6 MB
EGAF00005858521 tbi 1.6 MB
EGAF00005858522 tbi 1.6 MB
EGAF00005858523 tbi 1.7 MB
EGAF00005858524 tbi 1.7 MB
EGAF00005858525 tbi 1.6 MB
EGAF00005858526 tbi 1.6 MB
EGAF00005858527 tbi 1.7 MB
EGAF00005858528 tbi 1.6 MB
EGAF00005858529 tbi 1.6 MB
EGAF00005858530 tbi 1.7 MB
EGAF00005858531 tbi 1.7 MB
EGAF00005858532 tbi 1.6 MB
EGAF00005858533 tbi 1.7 MB
EGAF00005858534 tbi 1.7 MB
EGAF00005858535 tbi 1.7 MB
EGAF00005858536 tbi 1.7 MB
EGAF00005858537 tbi 1.7 MB
EGAF00005858538 tbi 1.6 MB
EGAF00005858539 tbi 1.7 MB
EGAF00005858540 tbi 1.6 MB
EGAF00005858541 tbi 1.7 MB
EGAF00005858542 tbi 1.6 MB
136 Files (14.7 GB)