Linkage disequlibrium in theDTNBP1 (dysbindin) gene region and on chromosome 1p36 among psychotic patients from a genetic isolate in Israel: Findings from identity by descent haplotype sharing analysis

2004 ◽  
Vol 128B (1) ◽  
pp. 65-70 ◽  
Author(s):  
Yoav Kohn ◽  
Eduardo Danilovich ◽  
Dvorah Filon ◽  
Ariella Oppenheim ◽  
Osnat Karni ◽  
...  
Keyword(s):  
Gene Region ◽  
Haplotype Sharing ◽  
Identity By Descent ◽  
Genetic Isolate ◽  
Linkage Disequlibrium ◽  
Chromosome 1P36

321-OR: A Genetic Locus on Chromosome 1p36 Associated with Cardiovascular Autonomic Neuropathy in Type 2 Diabetes

Diabetes ◽  
2019 ◽  
Vol 68 (Supplement 1) ◽  
pp. 321-OR
Author(s):  
YALING TANG ◽  
HETAL SHAH ◽  
XIUQIN SUN ◽  
BRUCE A. PERKINS ◽  
MICHAEL J. WAGNER ◽  
...  
Keyword(s):  
Type 2 Diabetes ◽  
Autonomic Neuropathy ◽  
Genetic Locus ◽  
Cardiovascular Autonomic Neuropathy ◽  
Chromosome 1P36

Regression Modelling of HLA Haplotype Sharing in Affected Siblings

Biometrics ◽  
1990 ◽  
Vol 46 (2) ◽  
pp. 427 ◽  
Author(s):  
G. A. Darlington ◽  
V. T. Farewell
Keyword(s):  
Haplotype Sharing ◽  
Regression Modelling

scholarly journals Analysis of Italian BRCA1/2 Pathogenic Variants Identifies a Private Spectrum in the Population from the Bergamo Province in Northern Italy

Cancers ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 532
Author(s):  
Gisella Figlioli ◽  
Arcangela De Nicolo ◽  
Irene Catucci ◽  
Siranoush Manoukian ◽  
Bernard Peissel ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Breast Cancer Risk ◽  
Cancer Risk ◽  
Disease Risk ◽  
Northern Italy ◽  
Genetic Isolate ◽  
National Population ◽  
Pathogenic Variants ◽  
High Breast Cancer Risk

Germline pathogenic variants (PVs) in the BRCA1 or BRCA2 genes cause high breast cancer risk. Recurrent or founder PVs have been described worldwide including some in the Bergamo province in Northern Italy. The aim of this study was to compare the BRCA1/2 PV spectra of the Bergamo and of the general Italian populations. We retrospectively identified at five Italian centers 1019 BRCA1/2 PVs carrier individuals affected with breast cancer and representative of the heterogeneous national population. Each individual was assigned to the Bergamo or non-Bergamo cohort based on self-reported birthplace. Our data indicate that the Bergamo BRCA1/2 PV spectrum shows less heterogeneity with fewer different variants and an average higher frequency compared to that of the rest of Italy. Consistently, four PVs explained about 60% of all carriers. The majority of the Bergamo PVs originated locally with only two PVs clearly imported. The Bergamo BRCA1/2 PV spectrum appears to be private. Hence, the Bergamo population would be ideal to study the disease risk associated with local PVs in breast cancer and other disease-causing genes. Finally, our data suggest that the Bergamo population is a genetic isolate and further analyses are warranted to prove this notion.

scholarly journals Fast and robust identity-by-descent inference with the templated positional Burrows-Wheeler transform

2020 ◽  
Author(s):  
William A Freyman ◽  
Kimberly F McManus ◽  
Suyash S Shringarpure ◽  
Ethan M Jewett ◽  
Katarzyna Bryc ◽  
...  
Keyword(s):  
Isolation By Distance ◽  
False Negative ◽  
Segment Length ◽  
Data Sets ◽  
Haplotype Sharing ◽  
Binary File ◽  
Inference Algorithms ◽  
Out Of Sample ◽  
Massive Scale ◽  
Burrows Wheeler Transform

Abstract Estimating the genomic location and length of identical-by-descent (IBD) segments among individuals is a crucial step in many genetic analyses. However, the exponential growth in the size of biobank and direct-to-consumer (DTC) genetic data sets makes accurate IBD inference a significant computational challenge. Here we present the templated positional Burrows-Wheeler transform (TPBWT) to make fast IBD estimates robust to genotype and phasing errors. Using haplotype data simulated over pedigrees with realistic genotyping and phasing errors we show that the TPBWT outperforms other state-of-the-art IBD inference algorithms in terms of speed and accuracy. For each phase-aware method, we explore the false positive and false negative rates of inferring IBD by segment length and characterize the types of error commonly found. Our results highlight the fragility of most phased IBD inference methods; the accuracy of IBD estimates can be highly sensitive to the quality of haplotype phasing. Additionally we compare the performance of the TPBWT against a widely used phase-free IBD inference approach that is robust to phasing errors. We introduce both in-sample and out-of-sample TPBWT-based IBD inference algorithms and demonstrate their computational efficiency on massive-scale datasets with millions of samples. Furthermore we describe the binary file format for TPBWT-compressed haplotypes that results in fast and efficient out-of-sample IBD computes against very large cohort panels. Finally, we demonstrate the utility of the TPBWT in a brief empirical analysis exploring geographic patterns of haplotype sharing within Mexico. Hierarchical clustering of IBD shared across regions within Mexico reveals geographically structured haplotype sharing and a strong signal of isolation by distance. Our software implementation of the TPBWT is freely available for non-commercial use in the code repository https://github.com/23andMe/phasedibd.

scholarly journals Reciprocal recombination and the evolution of the ribosomal gene family of Drosophila melanogaster.

Genetics ◽  
1989 ◽  
Vol 122 (3) ◽  
pp. 617-624 ◽  
Author(s):  
S M Williams ◽  
J A Kennison ◽  
L G Robbins ◽  
C Strobeck
Keyword(s):  
Drosophila Melanogaster ◽  
Gene Family ◽  
Ribosomal Rna ◽  
Natural Populations ◽  
Ribosomal Gene ◽  
Gene Region ◽  
Ribosomal Rna Gene ◽  
Reciprocal Recombination ◽  
Y Chromosomes ◽  
Length Polymorphisms

Abstract The role of reciprocal recombination in the coevolution of the ribosomal RNA gene family on the X and Y chromosomes of Drosophila melanogaster was assessed by determining the frequency and nature of such exchange. In order to detect exchange events within the ribosomal RNA gene family, both flanking markers and restriction fragment length polymorphisms within the tandemly repeated gene family were used. The vast majority of crossovers between flanking markers were within the ribosomal RNA gene region, indicating that this region is a hotspot for heterochromatic recombination. The frequency of crossovers within the ribosomal RNA gene region was approximately 10(-4) in both X/X and X/Y individuals. In conjunction with published X chromosome-specific and Y chromosome-specific sequences and restriction patterns, the data indicate that reciprocal recombination alone cannot be responsible for the observed variation in natural populations.

A HISTIDINE OPERATOR-CONSTITUTIVE MUTATION DECREASES THE FREQUENCY OF RECOMBINATION WITHIN THE HISTIDINE OPERON OF SALMONELLA TYPHIMURIUM

Genetics ◽  
1972 ◽  
Vol 71 (3) ◽  
pp. 461-464
Author(s):  
Dragutin J Savic
Keyword(s):  
Salmonella Typhimurium ◽  
Gene Region ◽  
Constitutive Mutation

Abstract A constitutive mutation in the histidine operon in Salmonella leads to a decrease in the recombinant recovery following transduction with P22 phage. This decrease appears to be a true decrease in recombination within the histidine operon and specific to that gene region. In addition, a strain with an unlinked mutation was isolated in which an operator-constitutive mutation is lethal.

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