Data Exploration and Summaries
Emmanuel Paradis in Population Genomics with R, 2020
Exploring data is an indispensable step before conducting model fitting or tests of hypotheses. It helps to assess the proportions of missing data, sample sizes per group, or the main patterns of variation in the data. Experience—and patience—are important during data exploration since some insights can be revealed by carefully looking at different facets of the data. Missing data can be a source of confusion, particularly with allelic data which can have several levels of complexity and where missing data can be coded in different ways. Pegas has a flexible framework with respect to missing data: most of the time, data are read “as is” in files. A useful approach to summarize information from a set of sequences is to first examine the sequences that are identical and calculate their frequencies. Pegas implements the class “haplotype” which works with different types of sequence data.
Serological Typing of HLA-A, -B, and -C Antigens
M. Kam, Jeffrey L. Bidwell in Handbook of HLA TYPING TECHNIQUES, 2020
The HLA-A, -B, and -C antigens are glycoproteins encoded by closely linked genes of the major histocompatibility complex (MHC) located on the short arm of chromosome 6 at 6p21.3 spanning a distance of approximately 3 × 10 6 bp. These genes are inherited en bloc as a haplotype and are codominantly expressed. Linkage disequilibrium is one of the main features of the HLA system. This is a phenomenon in which the observed frequency of alleles of different loci occurring together is greater in a population than expected by random chance, as calculated from the phenotype frequencies of the individual alleles. The definitive serological test to determine whether a patient is sensitized to antigens present on the lymphocytes of a particular donor is to perform a lymphocytotoxic cross-match. This will not indicate whether positivity is due to HLA or non-HLA antibodies, but the use of dithiothreitol will determine if an IgM or IgG antibody is responsible.
Pedigree and Linkage Analysis
Peter N. Robinson, Rosario M. Piro, Marten Jäger in Computational Exome and Genome Analysis, 2017
This chapter shows how the analysis of cosegregation in nuclear families (e.g., parents and siblings) can be used to filter genes and variants in WES/WGS studies. The family structure is recorded in PED files. The chapter begins with an explanation of the PED file format and the symbols used for describing a pedigree. Jannovar's strategy for performing pedigree analysis is to first group variants according to the gene they are located in. For larger pedigrees, classical linkage analysis is more powerful because it incorporates genetic map and allele frequency information and permits variable penetrance, non-parametric analysis and formal haplotype inference. If large pedigrees are available, linkage analysis can be performed prior to exome sequencing, and the linkage interval can be used to filter the exome results. Alternatively, linkage can be performed using single-nucleotide polymorphism (SNP) genotypes extracted from exome data.
Polymorphisms and haplotypes in VDR gene are associated with female idiopathic infertility
Published in Human Fertility, 2020
Jelena Djurovic, Gorana Stamenkovic, Jelena Todorovic, Natasa Aleksic, Oliver Stojkovic
Unexplained infertility refers to the absence of a definable cause of reproductive failure. Vitamin D receptor (VDR) acts as a transcription factor and regulates a number of vitamin D-responsive genes, including those involved in the immune system. Recent finding that VDR is expressed in reproductive tissues suggests a possible importance of vitamin D in pregnancy. We conducted a case-control study to examine the association of polymorphisms in VDR gene with reproductive success. DNA from 117 female patients with unexplained infertility and 130 fertile controls was isolated from peripheral blood and VDR genotypes (FokI, BsmI, ApaI and TaqI) were detected by PCR-RFLP. Haplotypes were determined using Haploview software. Our results show significant association of FokI and BsmI polymorphisms with infertility (p
Identification of genetic variants in TNF receptor 2 which are associated with the development of cervical carcinoma
Published in Biomarkers, 2016
Pallavi Singhal, Upma Sharma, Showket Hussain, Alo Nag, Mausumi Bharadwaj
Cervical cancer is one of the most common malignancies among women in India. Beside HPV, other factors present in host also put their role in the progression of cervical tumerogenesis. In present study, we screened 300 subjects to identify variations in TNFR2 gene by PCR-dHPLC method followed by direct sequencing. We identified six known and four novel variations in six different exons of TNFR2 gene. Out of these identified variations, five known variations were found to be significantly associated with the risk of cervical cancer (p
Association of angiotensin receptor 2 gene polymorphisms with pregnancy induced hypertension risk
Published in Hypertension in Pregnancy, 2018
Chenyang Li, Weijun Peng, Heng Zhang, Weirong Yan
Objectives: To investigate the association of polymorphisms and haplotypes of angiotensin receptor 2 (AT2R) gene with pregnancy induced hypertension (PIH) in Chinese Han women. Methods: A case-control study was designed with 446 cases (gestational hypertension, GH: 124; pre-eclampsia, PE + eclampsia, E: 322) and 650 controls. rs5193, rs1403543 and rs12710567 of AT2R gene were genotyped. A logistic regression approach was applied to estimate the relationship between the polymorphisms and haplotypes of AT2Rgene with PIH risk. Results: No relationship between AT2R gene polymorphisms and PIH was detected. The haplotype analysis also showed a negative result. Conclusions: rs5193, rs1403543 and rs12710567 of AT2R gene might have no effect on PIH risk among Chinese Han women.
Related Knowledge Centers
- Alleles
- Major Histocompatibility Complex
- Genotype
- Genetic Locus
- Genetics
- Locus
- Chromosome