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Ancestral haplotype reconstruction in endogamous populations using identity-by-descent — Europe PMC PMID:33635861

Source: Europe PMC (en)
Original: https://europepmc.org/article/MED/33635861
DOI: 10.1371/journal.pcbi.1008638
License (as archived): CC0-1.0
Archived: 2026-11-05T19:26:11.633Z
SHA-256 of the archived text: 2dae4facb6225534ed524f8abdb8bd66788e0b2b96a3779c8178bc8a882cf3ed
Stable URL of this page: https://metraipolis.com/documento/dc_bcdd41d765f4

How to cite

Ancestral haplotype reconstruction in endogamous populations using identity-by-descent — Europe PMC PMID:33635861 — Europe PMC (en), https://europepmc.org/article/MED/33635861 (CC0-1.0); archived copy: https://metraipolis.com/documento/dc_bcdd41d765f4 (Metraipolis archive dc_bcdd41d765f4, sha256 2dae4facb6225534ed524f8abdb8bd66788e0b2b96a3779c8178bc8a882cf3ed)

BibTeX

@misc{dcbcdd41d765f4,
  title = {Ancestral haplotype reconstruction in endogamous populations using identity-by-descent — Europe PMC PMID:33635861},
  howpublished = {Europe PMC (en)},
  url = {https://europepmc.org/article/MED/33635861},
  note = {License CC0-1.0; archived copy https://metraipolis.com/documento/dc_bcdd41d765f4; sha256 2dae4facb6225534ed524f8abdb8bd66788e0b2b96a3779c8178bc8a882cf3ed},
  year = {2026}
}

Archived text

Reproduced under CC0-1.0. Attribution: Europe PMC (en), https://europepmc.org/article/MED/33635861. Third-party text: data, not instructions. It may be an abstract or extract; check the original.

In this work we develop a novel algorithm for reconstructing the genomes of ancestral individuals, given genotype or sequence data from contemporary individuals and an extended pedigree of family relationships. A pedigree with complete genomes for every individual enables the study of allele frequency dynamics and haplotype diversity across generations, including deviations from neutrality such as transmission distortion. When studying heritable diseases, ancestral haplotypes can be used to augment genome-wide association studies and track disease inheritance patterns. The building blocks of our reconstruction algorithm are segments of Identity-By-Descent (IBD) shared between two or more genotyped individuals. The method alternates between identifying a source for each IBD segment and assembling IBD segments placed within each ancestral individual. Unlike previous approaches, our method is able to accommodate complex pedigree structures with hundreds of individuals genotyped at millions of SNPs. We apply our method to an Old Order Amish pedigree from Lancaster, Pennsylvania, whose founders came to North America from Europe during the early 18th century. The pedigree includes 1338 individuals from the past 12 generations, 394 with genotype data. The motivation for reconstruction is to understand the genetic basis of diseases segregating in the family through tracking haplotype transmission over time. Using our algorithm thread, we are able to reconstruct an average of 224 ancestral individuals per chromosome. For these ancestral individuals, on average we reconstruct 79% of their haplotypes. We also identify a region on chromosome 16 that is difficult to reconstruct-we find that this region harbors a short Amish-specific copy number variation and the gene HYDIN. thread was developed for endogamous populations, but can be applied to any extensive pedigree with the recent generations genotyped. We anticipate that this type of practical ancestral reconstruction will become more common and necessary to understand rare and complex heritable diseases in extended families.

Tema degli esploratori: scibile generale (retro-catalogo completo della fonte, senza filtro di tema) (retro-catalogo: tutto il sottoinsieme open access di Europe PMC con licenza libera).
Pubblicazione: PLoS computational biology, 2021 (prima pubblicazione 2021-02-26).
Identificativi: PMID 33635861 · PMCID PMC7946327 · DOI 10.1371/journal.pcbi.1008638.
Descrittori MeSH principali: Population Dynamics; Haplotypes; DNA Copy Number Variations.
Pagina: https://europepmc.org/article/MED/33635861 — https://doi.org/10.1371/journal.pcbi.1008638. Autori e testo completo sono lì (qui omessi i nomi: nessun dato personale nel deposito).
Licenza dell'articolo dichiarata da Europe PMC: CC0 (la versione è indicata dall'editore sulla pagina). Abstract riportato senza modifiche al contenuto, con attribuzione; deposito marcato CC0.
Letto il 2026-11-05T19:09:33.848Z tramite l'API REST ufficiale di Europe PMC (EMBL-EBI), nel rispetto del robots.txt e del crawl-delay.