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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.
DNA Methods in Veterinary Medicine
Published in Rebecca A. Krimins, Learning from Disease in Pets, 2020
Genome-wide association studies have been used in human genetics for several years to identify blocks of DNA with shared alleles, referred to as haplotypes, that are statistically associated with the risk for developing particular diseases. These haplotype blocks are shorter in larger and more outbred populations but are often much larger in more inbred populations because a relatively small founder population will have less heterogeneity and, therefore, a reduced opportunity for recombination events to break haplotypes at each generation. In humans, many of the first disease hunting GWAS studies were undertaken in populations that were genetically closed (e.g., Amish) or were relatively isolated (e.g., Iceland, Finland, etc.). Because such groups had gone through genetic bottlenecks it was reasoned that individuals with similar complex phenotypes might be more genetically similar to each other than individuals with those phenotypes in outbred populations. Haplotypes are also larger in newer populations where there has not been sufficient time for recombination. In humans, Europeans have larger haplotype blocks than Africans. Also, haplotypes are more alike in closely related family members. Within dog breeds, shared haplotypes are about as similar as those among human cousins (E. Karlsson, pers. comm.). These differences in haplotypes are used by commercial companies that genotype pets to identify their breed. Similarly, when we breed plants and animals for particular traits we lose heterogeneity. This can have both positive and negative consequences that can now be understood with DNA-based testing.
Serological Typing of HLA-A, -B, and -C Antigens
Published in M. Kam, Jeffrey L. Bidwell, Handbook of HLA TYPING TECHNIQUES, 2020
The Bw4 and Bw6 associations with the different B locus antigens (see Table 2) are useful in aiding typing assignment. For example, if a cell typed as B44 with Bw4 and Bw6, but no other serological reactions occurred for a second B locus antigen, certain conclusions can be drawn. The second B antigen may be B45, and unless monospecific B45 sera are on the typing tray, this would be masked by the B44 reaction pattern. The second B antigen could also be one of the B70 group of antigens, and unless B70+, B44- sera are on the typing tray, the B antigen would be masked by the B44. This point also applies to the situation in which a Bw6 associated antigen has been defined but the cell is typed as Bw4 and Bw6, and there are many antigen combinations to which this is applicable (see "Examples of Screening Results" and Table 2). For the typing assignment to be absolutely correct, a specificity should not be assigned unless sera are used to define that specificity, and assignment should not be based on the Bw4 and Bw6 associations. Family studies enabling the different haplotypes to be determined are useful in such circumstances. Assignment of antigens using the Bw4 and Bw6 associations may be necessary if the relevant sera or family members are not available.
HLA-A, -C, -B, -DRB1, -DQA1, and -DQB1 Allele and Haplotype Repertoires in the Albanian Population from Kosovo
Published in Immunological Investigations, 2022
Atifete Ramosaj-Morina, Marija Burek Kamenaric, Alije Keka Syla, Arbana Baloku, Zorana Grubic, Renata Zunec
Haplotype analysis can be used for understanding a population’s migration history. A possible origin was assigned to each of the most common haplotypes in our cohort, based on the highest frequencies of shared corresponding haplotypes within specific European and Mediterranean populations (Gonzalez-Galarza et al. 2015) and according to Martinez-Laso (Martinez-Laso et al. 2018). The proposed origin indicates the close relation of Albanians with European Mediterranean populations from the Iberian Peninsula across the Apennine Peninsula to the Balkan Peninsula and Anatolia and also reflects the history of Kosovo as a part of the Roman Empire, the Byzantine Empire, the Ottoman Empire and Yugoslavia. On the other hand, there are characteristics specific just to the Albanian population confirming their homogeneity and uniqueness. The example could be the unique haplotype for Kosovar Albanians, HLA-A*02:01~C*12:03~B*38:01~DRB1*04:02~DQA1*03:01~DQB1*03:02, present also with high frequency among Bosnia and Herzegovina minority and Croatian minority, suggesting that possible origin of this haplotype could be exactly from Kosovo and this wider area from where it then spread further towards east of the Europe. Additional proof could be the fact that more frequent haplotype in Europe, HLA-A*02:01~C*12:03~B*38:01~DRB1*13:01 was not observed in our cohort.
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).
What’s new in chronic pain pathophysiology
Published in Canadian Journal of Pain, 2020
Numerous mutation sites may cause a similar end phenotype or disease state. For example, cystic fibrosis is a disease that may result from any one mutation of more than 1000 described variants in the CFTR gene. These mutations can be as small as a single nucleotide polymorphism (SNP) in which a single base-pair substitution occurs in the genetic code at a specific point in the genome. This base pair can then have a downstream effect on the gene expression, including qualitative and quantitative defects of the resulting protein complexes. SNPs that occur together with high frequency are often referred to as a given haplotype. Haplotypes help identify other polymorphic sites on the same chromosome and are implicated in the pathogenesis of certain genetically linked disorders. There are more than 400 genes that encode human ion channels, and an almost endless number of permutations of mutations can occur.