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Genetic Counseling in Assisted Reproductive Technology
Published in Carlos Simón, Carmen Rubio, Handbook of Genetic Diagnostic Technologies in Reproductive Medicine, 2022
Unlike with prenatal diagnosis, with PGT-M, a test must be custom designed for each reproductive couple such that the at-risk and low-risk haplotypes can be defined. Determining the haplotypes involves assessing a set of genetic linkage markers shared among affected and/or unaffected first-degree relatives. The linkage markers (e.g., short tandem repeats [STRs]) flank the disease-causing variant within and around the gene. Linkage markers shared between the patient and an affected/carrier relative define the at-risk haplotype; genetic markers shared between the patient and an unaffected/non-carrier relative define the low-risk haplotype. Where possible, embryo testing involves assessing a combination of linkage markers as well as the disease-associated variant directly. If direct testing of the variant is not possible, PGT-M testing can often be carried out using linkage markers only, provided that the necessary relatives are available to provide samples for linkage analysis. The reason for this elaborate testing methodology is the limited number of cells that can be biopsied from a preimplantation embryo. Such a small sample number precludes many of the robust technologies available to directly detect the disease-causing variant in prenatal or pediatric/adult samples. Utilizing linkage analysis in combination with direct detection of the disease-causing variant, where possible, increases the accuracy of genetic testing applied to the extraordinarily small sample that can be obtained from preimplantation embryos.
Serological Typing of HLA-A, -B, and -C Antigens
Published in M. Kam, Jeffrey L. Bidwell, Handbook of HLA TYPING TECHNIQUES, 2020
In Tables 17 and 18 the antigen combinations or haplotypes observed to have a significant positive linkage disequilibrium are listed for these populations. The results in these tables are expressed as the delta values for the various haplotypes. Some haplotypes occur in many populations, while others appear to be restricted to particular ethnic groups. The extent to which a population study demonstrates the haplotypes in that population is obviously determined by the sample size. The haplotypes given in Tables 17 and 18 may not be definitive for those populations, but demonstrate the variation observed between different populations.
The Major Histocompatibility Complex
Published in Constantin A. Bona, Francisco A. Bonilla, Textbook of Immunology, 2019
Constantin A. Bona, Francisco A. Bonilla
It is often useful to consider a group of closely-linked highly polymorphic genetic loci as a unit. This is the basis of the concept of haplotype. The haplotype of the HLA loci is a designation describing the alleles present at all loci on one chromosome. An HLA haplotype is denoted simply by writing consecutively the specificities or alleles at each sublocus. An example of a haplotype might be: Al, B8, Cw7, DR3 (the identity of all loci need not be specified, depending on the circumstances). The haplotype designation is often useful in comparisons between individuals or populations defined by some characteristic. Because of the close linkage of the HLA loci, associations of particular alleles with biological markers of interest (a disease, for example) frequently extend to entire haplotypes. The biological significance of these associations depends on the particular marker(s) in question (see below).
Coffee Intake Interacted with the Bcl-2 rs1944420, rs7236090, and rs2849382 Haplotype to Influence Breast Cancer Risk in Middle-Aged Women
Published in Nutrition and Cancer, 2022
Meiling Liu, Sang Shin Song, Sunmin Park
A haplotype of the genetic variants was generated from related SNPs on the same chromosomes. In association analyses of genetic diseases, haplotype analysis can provide ancestral haplotype distributions. Furthermore, haplotype analysis involving several SNP sites is statistically more powerful than single SNP analysis. We analyzed haplotype frequencies using plink software, and divided participants by the haplotype allele frequencies into three categories (0-2, 4-6, and 7-12) by tertiles, that is, into the major allele of haplotype, heterozygote allele, and minor allele groups, respectively. The linkage disequilibrium (LD) plot of Bcl-2 rs1944420, rs7236090, and rs2849382 was plotted using Locus Zoom (Figure 1) to generate a single plot using a web form (http://csg.sph.umich.edu/locuszoom).
IL28B, TLR7 SNPs, and cytomegalovirus infection are risk factors for advanced liver disease in chronic hepatitis C patients
Published in Expert Review of Anti-infective Therapy, 2022
Fatma Omar Khalil, Ayman Alsebaey, Zeinab Abdelaziz Kasemy, Sabry Moawad Abdelmageed, Hanan Mosaad Bedair, Shimaa Abdelsattar
Statistical analyses were performed using SPSS version 22.0 (SPSS Inc., Chicago, IL, USA). Patient demographic data was expressed as mean ± SD. Pearson’s Chi-square (χ2) test was used to determine the significance of association between two categories. ANOVA test was used to compare among more than 2 groups for parametric data. Kruskal–Wallis test was used to compare among more than 2 groups as a non-parametric version of ANOVA. Post hoc test was used to detect least significant difference between the individual groups. Differences with a p-value of <0.05 were regarded as statistically significant. The two SNP haplotypes were inferred and analyzed. The 95% confidence interval (95% CI) and the odds ratio (OR) were consequentially calculated to assess the effects of alleles and haplotypes. Each SNP was tested for Hardy Weinberg equilibrium (HWE) between liver disease patients and controls. For additional analysis of the association between IL28B and TLR7 (rs179009) genes polymorphisms and ADHD, odds ratio was evaluated in various genetics models (dominant, recessive, co-dominant 1, co-dominant 2, and over-dominant).
Genetic variation patterns of β-thalassemia in Western Andalusia (Spain) reveal a structure of specific mutations within the Iberian Peninsula
Published in Annals of Human Biology, 2021
Luis J. Sánchez-Martínez, Candela L. Hernández, Juan N. Rodríguez, Jean M. Dugoujon, Andrea Novelletto, Paloma Ropero, Luisa Pereira, Rosario Calderón
Furthermore, the same four subjects presented similar genotypes (heterozygous) for the mutation arrays: CAP +20:C > T; CD2:T > C; IVS I-1:G; IVS I-6:T; IVS I-110:G; CD39:C; IVS II-16:G > C; IVS II-81:C > T; IVS II-666:C > T; IVS II-745:C > G; 71839:A. This finding suggests a shared origin, and when we referred to the family background of these people, they were all born in a small area (1270 km2) within Huelva Province known as “la Comarca del Condado.” Likewise, the analysis of the control population sample allowed us to observe that 61 individuals out of 97 analysed (62.89% of the total sample) shared the haplotype CAP +20:C; CD2:C; IVS I-1:G; IVS I-6:T; IVS I-110:G; CD39:C; IVS II-16:C; IVS II-81:C; IVS II-666:T; IVS II-745:C; 71839:A. The high population frequency of this haplotype is a particularity and is likely associated with the study population and zone. The allelic associations and statistical values in both patients and control samples are provided in Table S2.