Human leukocyte antigen (HLA) A-C-B-DRB1-DQB1 haplotype segregation analysis among 2152 families in China and the comparison to expectation-maximization algorithm result

According to doctors’ typing applications and laboratory standard operation procedure, sequence-based typing plus sequence-specific oligonucleotide probe methods were performed for high-resolution HLA-A, B, C, DRB1, and DQB1 typing for all patients. [...]the patients’ typing results were used as pha...

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Published in:Chinese medical journal Vol. 134; no. 14; pp. 1741 - 1743
Main Authors: Li, Yang, Chen, Lu-Yao, Zhang, Teng-Teng, Yuan, Xiao-Ni, Bao, Xiao-Jing, He, Jun
Format: Journal Article
Language:English
Published: China Lippincott Williams & Wilkins 26.03.2021
Lippincott Williams & Wilkins Ovid Technologies
Wolters Kluwer
Subjects:
Algorithms
Antigens
China
Clinical Observations
Genetics, Population
Haplotypes
HLA-A Antigens
HLA-B Antigens
HLA-C Antigens
HLA-DQ beta-Chains
HLA-DRB1 Chains - genetics
Humans
Motivation
Segregation
Software
China
ISSN:0366-6999, 2542-5641, 2542-5641
Online Access:Get full text
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Summary:According to doctors’ typing applications and laboratory standard operation procedure, sequence-based typing plus sequence-specific oligonucleotide probe methods were performed for high-resolution HLA-A, B, C, DRB1, and DQB1 typing for all patients. [...]the patients’ typing results were used as phase-known and phase-unknown data to obtain observed and expected HFs, respectively, by the direct counting EM algorithm (only HFs >1 × 10–5 were outputted by Arlequin). The P values of the Chi-square test showed that there were no statistically significant differences between observed and expected haplotypes, not only in total overlapping data (P = 0.2424) and common data (HF ≥ 0.1%, P = 0.3698) but also in less-common data (HF < 0.1%, P = 0.1582). [...]the tendencies of observed and expected haplotypes are coincident, and the tendency concordance of common data is the best; then, the total overlapping data last the less common data. [...]EM could miss less-common real haplotypes but built incorrectly less-common haplotypes. [...]identifying less common haplotypes from segregation analysis must be used for checking and as supplements to cover the shortage of EM.
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ISSN:0366-6999
2542-5641
2542-5641
DOI:10.1097/CM9.0000000000001458