Understanding Mendelian errors in SNP arrays data using a Gochu Asturcelta pig pedigree: genomic alterations, family size and calling errors.

Autor: Arias KD; Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, 33394, Gijón, Asturias, Spain., Álvarez I; Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, 33394, Gijón, Asturias, Spain., Gutiérrez JP; Departamento de Producción Animal, Universidad Complutense de Madrid, Avda. Puerta de Hierro s/n, 28040, Madrid, Spain., Fernandez I; Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, 33394, Gijón, Asturias, Spain., Menéndez J; ACGA, C/ Párroco José Fernández Teral nº 5 A, 33403, Avilés, Asturias, Spain., Menéndez-Arias NA; Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, 33394, Gijón, Asturias, Spain., Goyache F; Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, 33394, Gijón, Asturias, Spain. fgoyache@serida.org.
Jazyk: angličtina
Zdroj: Scientific reports [Sci Rep] 2022 Nov 16; Vol. 12 (1), pp. 19686. Date of Electronic Publication: 2022 Nov 16.
DOI: 10.1038/s41598-022-24340-0
Abstrakt: Up to 478 Gochu Asturcelta pig parents-offspring trios (61 different families) were genotyped using the Axiom_PigHDv1 Array to identify the causes of Mendelian errors (ME). Up to 545,364 SNPs were retained. Up to 40,540 SNPs gathering 292,297 allelic mismatches were identified and were overlapped with SINEs and LINEs (Sscrofa genome 11.1). Copy number variations (CNV) were called using PennCNV. ME were classified into eight different classes according to the trio member ("Trio" meaning no assignment) and the allele on which ME was identified: TrioA/B, FatherA/B, MotherA/B, OffspringA/B. Most ME occurred due to systematic causes: (a) those assigned to the Father, Mother or Offspring occurred by null or partial null alleles characterized by heterozygote deficiency, varied with family size, involved a low number of loci (6506), and gathered most mismatches (228,145); (b) TrioB errors varied with family size, covaried with SINEs, LINEs and CNV, and involved most ME loci (33,483) and mismatches (65,682); and (c) TrioA errors were non-systematic ME with no sampling bias involving 1.2% of mismatches only and a low number of loci (1939). The influence of TrioB errors on the overall genotyping quality may be low and, since CNV vary among populations, their removal should be considered in each particular dataset. ME assignable to the Father, Mother or Offspring may be consistent within technological platforms and may bias severely linkage or association studies. Most ME caused by null or partial null alleles can be removed using heterozygote deficiency without affecting the size of the datasets.
(© 2022. The Author(s).)
Databáze: MEDLINE
Externí odkaz:
Nepřihlášeným uživatelům se plný text nezobrazuje