China
Africa
Explore chapters and articles related to this topic
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
The output of the CE is converted to an electropherogram (epg) using visualization or analysis software. A representation of a hypothetical epg is found in Figure 1.1. In Figure 1.1 the two STR loci D16S539 and D2S1338 are amplified in the blue dye channel (FAM). In the circle below the peaks, we observe three numbers. The top number is the number of repeats within the allele. This value is often called the “allele number” for the STR marker. For D16S539, there are two alleles, 9 and 11 (a heterozygous genotype), and for D2S1338, we observe one peak, 20, which can also be expressed as the homozygous 20,20 genotype. The second (middle number) in the circle represents the relative fluorescent units (rfu) of the peaks in the profile. The rfu is a relative measurement of the signal (on the y-axis) generated by the fluorescent dyes when they were excited by the laser during electrophoresis. This value is often called the “peak height” of the allele. Peak height is relative to the amount of DNA (template), and in general, the greater the signal generated, the more copies of DNA were amplified.
Molecular Diagnosis of Autosomal Dominant Polycystic Kidney Disease
Published in Jinghua Hu, Yong Yu, Polycystic Kidney Disease, 2019
Matthew Lanktree, Amirreza Haghighi, Xueweng Song, York Pei
Regardless of the sequencing technology employed, putative variants in cystogenic genes will be identified that will require evaluation for pathogenicity. Quality control starts with examination of the electropherogram in capillary sequencing, or coverage, read depth, and sequencing quality scores in next generation sequencing technology. A BLAST search should be performed to determine if the variant sequence is found within pseudogene sequence, and thus likely due to a sequencing error. Next, identification of presence and frequency of the mutation in published control and case populations, cosegregation of the variant through family members when available, and bioinformatic prediction is required. Finally, creation of cell- or animal-based models can be considered.
Principles of forensic science and crime scene investigation
Published in Jason Payne-James, Richard Jones, Simpson's Forensic Medicine, 2019
Jason Payne-James, Richard Jones
The loci that are amplified vary in the number of repeats that are commonly encountered and so a range in size and thus molecular weight exists. The sample is subjected to capillary electrophoresis in a genetic analyser across a high potential difference. This means that the low molecular weight alleles pass through the capillaries and are detected more rapidly than those of a higher molecular weight. As each of the STR alleles have been tagged with a fluorescent dye, they are detected as they pass a laser detector. The time of detection, calibrated against a molecular weight standard, and the particular dye label enables a range of STRs to be analysed in the same sample. As each allele passes the laser, it registers as a peak in intensity of the fluorescent dye. This is translated into an electropherogram (EPG) which represents a DNA profile as a series of peaks along a graphical line (Figure 21.4).
The obesity associated FTO gene polymorphism and the risk of preeclampsia in Iranian women: A case–control study
Published in Hypertension in Pregnancy, 2023
Ghasem Azizi-Tabesh, Hossein Sadeghi, Arezoo Farhadi, Mohammad Foad Heidari, Aghdas Safari, Mehdi Shakouri Khomartash, Javad Behroozi, Saeid Doaei, Maryam Gholamalizadeh
The genotypes of the FTO rs9939609 SNP were analyzed using TP-ARMS-PCR and subsequent gel electrophoresis. An electropherogram of different genotypes is shown in Figure 1. Three genotypes were detected based on their band sizes. The heterozygous (AT) genotype showed three bands: 194 bp, 278 bp, and 429 bp. Homozygous (TT) genotype revealed two bands: 278 bp and 429 bp, as well as homozygous (AA) genotype indicated by two bands: 194 bp and 429 bp. The results obtained from genotyping using TP-ARMS-PCR were in concordance with the sequencing results Figure 2. In contrast to PE patients, healthy controls had a genotype distribution that was consistent with the Hardy-Weinberg principle. In women with PE, homozygous genotype AA of rs9939609 is statistically significantly less common than in controls: 2.3 versus 15.2%. The distribution of genotypes of the studied SNP is graphically illustrated in Figure 3. The results showed that FTO rs9939609 was associated with PE in codominant, dominant, and recessive genetic models. The recessive model with the lowest AIC and BIC values was considered the best-fit model (Table 3). Binary logistic regression analysis showed that the AA genotype of rs9939609 exhibited a protective role against PE (adjusted OR = 0.046, 95% CI: 0.004-0.469, p = 0.009) after adjusting for age, BMI, and gestational age (Table 4).
Copy number variation analysis using next-generation sequencing identifies the CFHR3/CFHR1 deletion in atypical hemolytic uremic syndrome: a case report
Published in Hematology, 2022
Joonhong Park, Ho-Young Yhim, Kyung Pyo Kang, Tae Won Bae, Yong Gon Cho
Multiplex ligation-dependent probe amplification (MLPA) was performed to confirm the CFHR3/CFHR1 deletion identified by NGS with CNV analysis using a SALSA® MLPA® Probemix P236-A3 ARMD mix-1 (MRC-Holland, Amsterdam, The Netherlands) according to the manufacturer’s protocol. Capillary electrophoresis and fragment analysis were conducted on the 3730XL Genetic Analyzer (Applied Biosystems, Carlsbad, CA, USA). The electropherogram data were analyzed using GeneMarker software ver. 3.0.1 (Softgenetics, State College, PA, USA) according to the manufacturer’s instructions. The resulting peak intensities were normalized to those of the sex-matched normal DNA and manufacturer control probes as a reference. A probe-to-peak ratio between 0.8 and 1.2 was defined as a normal copy number (wild-type), and a ratio between 0.4 and 0.65 represented a heterozygous deletion (loss of one copy number).
Diagnostic profile of the AmplideX Fragile X Dx and Carrier Screen Kit for diagnosis and screening of fragile X syndrome and other FMR1-related disorders
Published in Expert Review of Molecular Diagnostics, 2021
Elizabeth Berry-Kravis, Lili Zhou, Jonathan Jackson, Flora Tassone
The AmplideX Fragile X Dx & Carrier Screen Kit reports all detected FMR1 alleles for each sample and determines the associated genotype category based on the longest detected allele. The assay does not distinguish between mosaic and non-mosaic alleles. Due to the challenges associated with size mosaicism, when the assay detects more than one (1) peak for a male or more than two (2) peaks for a female, the electropherogram should be carefully inspected to confirm the presence of size mosaicism. The assay has been validated to detect alleles above a defined fraction with 95% frequency, on an allele-specific basis; however, mosaic alleles may still be detected below these levels, albeit at a reduced frequency. Laboratories may consider additional testing to confirm mosaicism for alleles of different sizes. Size mosaicism detected in blood may not reflect mosaicism in other tissues. The significance of size mosaicism should be interpreted with caution in conjunction with other laboratory and clinical information (e.g., sex of patient, diagnostic testing or carrier screening, patient symptoms) and should include consultation with a genetic professional.