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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.
Human Skeletal Remains
Published in Cristoforo Pomara, Vittorio Fineschi, Forensic and Clinical Forensic Autopsy, 2020
Francesco Sessa, Dario Piombino-Mascali, Nicholas Márquez-Grant, Luigi Cipolloni, Cristoforo Pomara
The main aim of DNA analysis is short tandem repeat (STR) typing that can identify the victim: Only if this attempt fails, various purification methods, mtDNA sequencing, or SNP analysis, that are now available can be employed (Bender et al., 2000; Holland et al., 2015). Obviously, the identification process refers to identifying an unknown person, and can be applied only if there are relatives or personal objects of the suspected decedent (Butler, 2005; Butler et al., 2007; Budowle et al., 2009; Templeton et al., 2013).
An Introduction and Review of DNA Profile Interpretation
Published in Jo-Anne Bright, Michael D. Coble, Forensic DNA Profiling, 2019
Jo-Anne Bright, Michael D. Coble
STR markers contain a repeating unit (called the motif) that is composed of four nucleotide bases, such as AGTC or ATTC. These “tetranucleotide” markers (tetra meaning four) make up the majority of STRs used in forensic testing, although there is now a common locus that has three nucleotide repeats (D22S1045, a trinucleotide repeat [tri meaning three]). Having three, four, or five repeating nucleotides within the repeating structure is why these markers are called “short” tandem repeats.
Fast-tracking antibody maturation using a B cell-based display system
Published in mAbs, 2022
Hitomi Masuda, Atsushi Sawada, Shu-ichi Hashimoto, Kanako Tamai, Ke-Yi Lin, Naoto Harigai, Kohei Kurosawa, Kunihiro Ohta, Hidetaka Seo, Hiroshi Itou
In the case of D058, 42.5% of the viable clones (31 of 72 clones) exhibited improved antigen reactivity and 15 antibodies with unique V regions were obtained. Amino acid insertions and deletions were frequently observed in VH CDR2 of the clones. A tandem repeat in the corresponding region was identified and the insertion and deletion of the amino acids were found near the repeated sequence (Figure S3). Such tandem repeats promote intermediate loop formation resulting in nucleotide deletions and duplications during repair.35 As multiple AID hotspots are identified in this region, AID deamination is likely to accelerate this deletion and duplication. Indeed, such mutations have been reported in human immune system35 and other cell-based affinity maturation platforms utilizing AID-mediated SHM.17 Thus, the deletion and insertion observed in VH CDR2 of D058 are in line with the mutational characteristics resulting from AID-mediated SHM.
Prevalence and characterisation of size and sequence-based microvariant alleles at nine autosomal STR markers in the Central Indian population
Published in Annals of Human Biology, 2021
Hirak Ranjan Dash, Kamayani Vajpayee, Ankit Srivastava, Surajit Das
The current day gold standard of forensic DNA analysis relies on exploring the repeatability of Short Tandem Repeat (STR) markers in human DNA to generate a unique profile. STR loci are found scattered more evenly throughout the genome constituting around 3% of the total genome (Fan and Chu 2007). After completion of the human genome project, ∼700,000 STR loci have been characterised out of which STR loci with two and three nucleotide repeat-units are found to be more prevalent in comparison to tetra-, penta- or hexa- nucleotide STRs (Willems et al. 2014). Despite a huge occurrence of STRs in the human genome, the current recommendation includes only 20 STR markers of either tri- or tetra- nucleotide repeats for forensic DNA analysis (Hares 2015). The well-characterised STR markers with stand-out population-specific forensic and paternity parameters have been included in the list of core loci.
Use of chimerism analysis after allogeneic stem cell transplantation: Belgian guidelines and review of the current literature
Published in Acta Clinica Belgica, 2021
Anke Delie, Anke Verlinden, Karolien Beel, Dries Deeren, Dominiek Mazure, Frédéric Baron, Dimitri Breems, Ann De Becker, Carlos Graux, Philippe Lewalle, Johan Maertens, Xavier Poire, Helene Schoemans, Dominik Selleslag, Florence Van Obbergh, Tessa Kerre
Short tandem repeats are units of 2 to 6 base pairs in length repeated multiple times within a given DNA fragment. These DNA fragments have a highly polymorphic nature between individuals, with a variable number of repeats at each tested locus. By using PCR-based amplification of these loci, patient and donor DNA can be identified based on the length of the resulting PCR products [2,9–12]. There are several commercial kits available with up to 16 STR markers, originally designed for use in forensic identification, which cover multiple ethnic backgrounds [2,9,12]. Short tandem repeat based chimerism analysis has a reported sensitivity of 1-5% [1,10,11,13] with a high reproducibility and an applicability (or informativity, i.e. the number of donor/recipient couples that can be evaluated using this technique) of nearly 100% [14]. (Table 2)