HLA Haplotypes in Families by NGS
Project leaders: Medhat Askar & Kazutoyo Osoegawa
Anthropological study of families by NGS of full-length HLA genes to determine haplotype segregation in multiple populations. Samples from family quartets consisting of two parents and at least two non-HLA identical children or family trios consisting of one parent and at least two non-HLA identical children, two parents and one child or 2 parents and multiple HLA identical children are required. The families should be previously HLA typed at any level (serology, DNA). Investigators may submit samples only or samples and NGS data.
Milestones in years:
2019: Submission of sample profiles and other pertinent data and preliminary analysis
2020 (Jan – July): Testing of samples that need confirmatory NGS testing and further analysis
2020 (Aug – Dec): Re-analyze HLA genotypes using organizer defined IPD-IMGT database version
2021: Final analysis and preparation of final report for presenting during the workshop
Patient/sample description (if applicable, details, inclusion/exclusion criteria):
HLA typing results of samples from family quartets consisting of two parents and at least two non-HLA identical children or family trios consisting of one parent and at least two non-HLA identical children are required.
Data required (number, type of data, inclusion/exclusion criteria):
Pedigree analysis including relations of all subjects tested
NGS testing results of all family members
Fastq files of samples tested by NGS
Any pertinent information to the subject carrying the allele of interest such as ethnic background
No max or min number of samples required
Samples required (if applicable, number, type of samples, inclusion/exclusion criteria):
For samples not tested by NGS, 2 ug DNA of high quality suitable for long range PCR amplification.
Reagents/additional assays required:
Data infrastructure required:
A database that house the collected typing results and fastq files similar to the database provided by the Stanford group during the 17th IHIW. In addition, the consensus sequences of all alleles identified in members of families will be confirmed by comparing sequences of the same allele identified in multiple subjects carrying the same allele (established by segregation) in combination with different alleles.