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Preimplantation Genetic Diagnosis for Single Gene Disorders
Published in Carlos Simón, Carmen Rubio, Handbook of Genetic Diagnostic Technologies in Reproductive Medicine, 2022
Ana Cervero, Jose Antonio Martínez-Conejero, Lucía Sanz-Salvador, Claudia Gil-Sanchís, Maribel Sánchez-Piris, Laura Iñiguez Quiles
The different approaches that are employed in PGT-M are based on haplotyping. Genetic markers, short tandem repeats (STRs), or single nucleotide polymorphisms (SNPs) located close to the gene of interest are analyzed in DNA samples from the reproductive couple and relevant relatives during the preclinical work-up or pre-PGT-M test. The haplotype which is present in the family members with the familial pathogenic variant is named the at-risk haplotype, whereas the haplotype without the familial pathogenic variant is referred to as the wild-type or low-risk haplotype. During pre-PGT-M work-up, the analysis of polymorphic markers in DNA samples from patients and other relatives identifies which alleles are expected in the embryos, and the specific marker alleles which co-segregate with the mutation. This combined approach improves accuracy, minimizing potential errors caused by undetected allele drop out (ADO) or contamination (20). ADO refers to the amplification failure (or extreme preferential non-amplification) of one of the two alleles, making a heterozygous locus appear homozygous, and potentially leading to misdiagnosis. The clinical test can be either direct, when the pathogenic variant plus linked genetic markers are assessed, or indirect, when testing is based on haplotyping only. Recently, the ESHRE PGT Consortium published a paper providing recommendations on the technical aspects of PGT-M, covering recommendations on basic methods for PGT-M and testing strategies (21).
Medicolegal Investigation of Deaths
Published in Kevin L. Erskine, Erica J. Armstrong, Water-Related Death Investigation, 2021
Human DNA has numerous, short nonfunctional repetitive locations or loci. The short repetitive loci are known as short tandem repeats (STRs) and form patterns that are unique to each individual. They are known for their stability and withstand harsher environmental conditions. Following laboratory techniques that extract, copy, and separate the DNA from the biological sample, the STR DNA typing technique is applied in order to obtain a profile based on the identification of a number of unique regions called loci (Figure 6.6). 3,4 Once obtained, this unique profile can be subsequently compared to the victim’s DNA for the purpose of inclusion or exclusion of the victim, as the individual that was in contact with an object such as a weapon or was wearing or in contact with an item of clothing.3,4 Similarly, the DNA profile extracted from a biological sample submitted from a crime scene can be compared to the suspect to include or exclude that individual’s involvement in a crime or presence at a scene. Biological material, including blood, may also be submitted from the victim at the time of autopsy, serving as a DNA standard or reference sample to which other DNA-containing biological samples obtained elsewhere can be compared.
Preimplantation Genetic Testing for Monogenic Disorders
Published in Darren K. Griffin, Gary L. Harton, Preimplantation Genetic Testing, 2020
Martine De Rycke, Pieter Verdyck
In practice, PGT-M with multiplex PCR can be subdivided in informativity testing, multiplex PCR optimization, and the actual clinical PGT cycle. For informativity testing, DNA and genetic reports from the couple and relevant family members are collected. STR markers located close to the gene of interest are genotyped to allow for selection of informative STR markers that flank the gene of interest. Preferably, the selected STR markers allow discrimination of all parental haplotypes. The haplotype that is shared between the relatives carrying the familial mutation is then inferred as the risk haplotype. If the risk haplotype is determined during workup, an indirect strategy can be chosen using STR markers only for the clinical PGT cycle. Alternatively, a direct strategy is possible where the detection of the mutation(s) is added to the STR markers for confirmation of phasing [14].
Genetic diversity of 23 STR loci of the Guizhou Tujia ethnic minority and the phylogenetic relationships with 22 other populations
Published in Annals of Human Biology, 2023
Shuhua Li, Siyu Chai, Limei Yu, Tao Zhang, Zulin Liu, Yinlei Lei, Kaiqin Chen, Hao Zhang, YanFei Liu, Pengyu Chen
Short tandem repeats (STRs) are repetitive nucleotide sequences ranging from 2 to 6 base pairs widely distributed throughout the human genome (Edwards et al. 1991; Ellegren 2004; Jobling and Gill 2004; Chen et al. 2018). Due to their high level of polymorphic information, STR markers have become the gold standard in forensic DNA analysis, especially in human identification and paternity testing, surpassing other DNA markers such as single nucleotide polymorphisms (SNPs) (Zhang 2015; Yao and Wang 2016; He et al. 2018; Wu et al. 2020). In recent years, new commercial multiple STR detection systems containing more autosomal STRs have been developed to further improve their discriminating ability with the increasing growth of forensic DNA databases. Additionally, STRs are frequently used in human population genetics to predict the population genetic structure of geographically and ethno-linguistically diverse subpopulations via genetic affinity analysis (Gao et al. 2021; Kumar et al. 2021; Tran et al. 2021; Wang et al. 2021; Chandra et al. 2022).
Geolocation prediction from STR genotyping: a pilot study in five geographically distinct global populations
Published in Annals of Human Biology, 2023
Mansi Arora, Hirak Ranjan Dash
STR markers are highly versatile and have been extensively studied for their individualisation capabilities in various populations. Autosomal STR markers, mini-STRs (Nieuwerburgh et al. 2014), Y-STR haplotype prediction (Kayser 2017), X-STR analysis in sample limiting conditions (Yang et al. 2017), and rapidly mutating (RM) STRs for individualisation (Ballantyne et al. 2014) have been widely used for forensic DNA analysis purposes. STR analysis is being performed to solve cases such as paternity disputes, identification, murder, sexual assault, etc. without giving any investigative leads. The use of such markers in other applications besides individualisation has been explored a little to date, such as monitoring of haematopoietic chimerism in patients after allogeneic stem cell transplantation (Tilanus 2006), matching between organ donor and recipients (Mishra et al. 2020) and cell line identification (Reid et al. 2017).
Genetic diversity of 15 STR loci in Yunnan Va ethnic minority and the phylogenetic relationships with 26 other populations
Published in Annals of Human Biology, 2022
Xiufeng Zhang, Jing Li, Jingtao Wen
Genomic DNA was extracted with the Chelex-100 method and amplified with the AmpFlSTR®Identifiler™ (Applied Biosystems) PCR Amplification kit on GeneAmp PCR system 9700 (Thermo Fisher) according to the manufacturer’s recommendations (Walsh et al. 1991). 25 μL reaction volume was used for each sample, which contains 10.5 μL PCR reaction mix, 5.5 μL Primer set, 0.5 μL Taq Gold DNA polymerase, 7.5 μL ddH2O, and 1.0 μL template DNA. PCR conditions had the following steps: pre-denatured 95 °C for 11 min, followed by 28 cycles of 94 °C for 1 min, 59 °C for 1 min, 72 °C for 1 min, a final extension hold at 60 °C for 60 min and a final soak at 4 °C. Amplified products were genotyped on a 3130xl Genetic Analyser (Applied Biosystems). The electrophoretic sampling mixture included 1.0 μL amplified product, 8.7 μL Hi-Di formamide and 0.3 μL Gene ScanTM 500 LIZ Size Standard. Raw data analysis for STR was performed with the GeneMapper ID v3.2 software (Applied Biosystems).