We describe a novel approach for evaluating SNP genotypes of a genome-wide association scan to identify "ethnic outlier" subjects whose ethnicity is different or admixed compared to most other subjects in the genotyped sample set. Each ethnic outlier is detected by counting a genomic excess of "rare" heterozygotes and/or homozygotes whose frequencies are low (<1%) within genotypes of the sample set being evaluated. This method also enables simple and striking visualization of non-Caucasian chromosomal DNA segments interspersed within the chromosomes of ethnically admixed individuals. We show that this visualization of the mosaic structure of admixed human chromosomes gives results similar to another visualization method (SABER) but with much less computational time and burden. We also show that other methods for detecting ethnic outliers are enhanced by evaluating only genomic regions of visualized admixture rather than diluting outlier ancestry by evaluating the entire genome considered in aggregate. We have validated our method in the Wellcome Trust Case Control Consortium (WTCCC) study of 17,000 subjects as well as in HapMap subjects and simulated outliers of known ethnicity and admixture. The method's ability to precisely delineate chromosomal segments of non-Caucasian ethnicity has enabled us to demonstrate previously unreported non-Caucasian admixture in two HapMap Caucasian parents and in a number of WTCCC subjects. Its sensitive detection of ethnic outliers and simple visual discrimination of discrete chromosomal segments of different ethnicity implies that this method of rare heterozygotes and homozygotes (RHH) is likely to have diverse and important applications in humans and other species.
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http://dx.doi.org/10.1093/hmg/ddq102 | DOI Listing |
Cureus
December 2024
Internal Medicine, National Hospital of Sri Lanka, Colombo, LKA.
Hereditary hemochromatosis occurs due to genetic mutations, namely, cysteine-to-tyrosine substitution at amino acid 282 (C282Y) and histidine-to-aspartic acid substitution at 63 (H63D) mutations. The role of H63D mutation in hemochromatosis is less clear, and its penetrance is low even in homozygotes. Therefore, iron overload in H63D heterozygotes is extremely rare and scarcely reported.
View Article and Find Full Text PDFGenes (Basel)
January 2025
Ophthalmology Department, Federal University of São Paulo, São Paulo 04039-032, Brazil.
Background: Nance-Horan syndrome (NHS) is a rare, frequently underdiagnosed, X-linked disease caused by mutations in the NHS gene. In males, it causes bilateral dense pediatric cataracts, dental anomalies, and facial dysmorphisms. Females traditionally have a more subtle phenotype with discrete lens opacities as an isolated feature.
View Article and Find Full Text PDFGenet Test Mol Biomarkers
January 2025
Department of Biology, University of Sistan and Baluchestan, Zahedan, Iran.
Fanconi anemia (FA) is a rare genetic disorder that affects multiple systems in the body and is the most prevalent congenital syndrome, leading to bone marrow failure. Twenty-two genes have been identified as contributors to the disease. Significant advancements have been made in the past 2 decades in understanding the genetic and pathophysiological processes involved.
View Article and Find Full Text PDFClin Oral Implants Res
January 2025
Second Dental Center, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
Objectives: WNT10A mutations are associated with tooth agenesis. This study aimed to assess the clinical outcomes of dental implants in patients carrying WNT10A mutations with different molecular statuses and phenotypes over a long-term follow-up period.
Materials And Methods: Patients with tooth agenesis were screened by whole-exome sequencing (WES) from January 2010 to September 2023.
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