Five cases of forensic short tandem repeat DNA typing

Schmitt, Cornelia; Benecke, Mark

doi:10.1002/elps.1150180506

Cited by 15 publications

(9 citation statements)

References 35 publications

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“…In theory, testing haplotypes could allow one to identify the presence of suspect in a large mixture of DNAs, such as in polysuspect cases. 35,36 In addition to forensic applications, tools for quality control and sample tracking in a large inventory of human DNA samples would be valuable. Such tools have previously been reported using panels of SNPs, 37 and the NGS-haplotyping assay could be applied in similar situations.…”

Section: The Human Genome Contains Clusters Of Snps That Can Be Amplimentioning

confidence: 99%

Haplotype Counting by Next-Generation Sequencing for Ultrasensitive Human DNA Detection

Debeljak

Freed

Welch

et al. 2014

The Journal of Molecular Diagnostics

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The ASCP designates this journal-based CME activity ("JMD 2014 CME Program in Molecular Diagnostics") for a maximum of 48 AMA PRA Category 1 Credit(s)ä. Physicians should only claim credit commensurate with the extent of their participation in the activity. CME Disclosures: The authors of this article and the planning committee members and staff have no relevant financial relationships with commercial interests to disclose. Human identity testing is critical to the fields of forensics, paternity, and hematopoietic stem cell transplantation. Most bone marrow (BM) engraftment testing currently uses microsatellites or short tandem repeats that are resolved by capillary electrophoresis. Single-nucleotide polymorphisms (SNPs) are theoretically a better choice among polymorphic DNA; however, ultrasensitive detection of SNPs using next-generation sequencing is currently not possible because of its inherently high error rate. We circumvent this problem by analyzing blocks of closely spaced SNPs, or haplotypes. As proof-ofprinciple, we chose the HLA-A locus because it is highly polymorphic and is already genotyped to select proper donors for BM transplant recipients. We aligned common HLA-A alleles and identified a region containing 18 closely spaced SNPs, flanked by nonpolymorphic DNA for primer placement. Analysis of cell line mixtures shows that the assay is accurate and precise, and has a lower limit of detection of approximately 0.01%. The BM from a series of hematopoietic stem cell transplantation patients who tested as all donor by short tandem repeat analysis demonstrated 0% to 1.5% patient DNA. Comprehensive analysis of the human genome using the 1000 Genomes database identified many additional loci that could be used for this purpose. This assay may prove useful to identify hematopoietic stem cell transplantation patients destined to relapse, microchimerism associated with solid organ transplantation, forensic applications, and possibly patient identification. Myeloablative conditioning and allogeneic stem cell transplantation have historically been limited to the treatment of lethal hematological malignancies in children or young adults. More recently, with the advent of highly immunosuppressive, nonmyeloablative regimens, the clinical use of allogeneic stem cell transplantation has expanded to include older, less fit patients with hematological malignancies and patients with nonmalignant disorders, such as sickle-cell disease.1e4 Nonmyeloablative conditioning regimens offer the additional safeguard of recovery of autologous hematopoiesis in the event of graft rejection and may be a safer option in patients at risk for immune-mediated rejection of the donor graft.Chimerism testing at set intervals is an effective method for detecting graft rejection or recurrence of the original hematopoietic neoplasm after allogeneic hematopoietic stem cell transplantation (

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Section: The Human Genome Contains Clusters Of Snps That Can Be Amplimentioning

confidence: 99%

Haplotype Counting by Next-Generation Sequencing for Ultrasensitive Human DNA Detection

Debeljak

Freed

Welch

et al. 2014

The Journal of Molecular Diagnostics

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“…21 The National Institute of Standards and Technology has compiled and maintained a Short Tandem Repeat DNA Internet Database (http://www.cstl. nist.gov/biotech/ strbase/) since 1997 for the purpose of DNA typing in forensic study.…”

Section: Discussionmentioning

confidence: 99%

Short tandem repeat polymorphism in a novel esophageal cancer‐related gene (ECRG2) implicates susceptibility to esophageal cancer in Chinese population

Yue

Tan

et al. 2003

Intl Journal of Cancer

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We have previously cloned and identified a novel esophageal cancer related gene 2 (ECRG2; GenBank Accession Number AF268198), which is down-regulated in esophageal squamous cell carcinoma (ESCC) and involved in the induction of the apoptosis in esophageal cancer cell lines. In the present study, we have found a short tandem repeat (STR) polymorphism in the noncoding region of the exon 4 of the ECRG2 gene by using PCR-denaturing high-performance liquid chromatography (DHPLC Esophageal cancer, with a 5-year survival rate Ͻ10%, is one of the most common fetal cancers worldwide and occurs at very high frequencies in certain areas of China, Iran, South Africa, Uruguay, France and Italy. 1 Fifty percent of esophageal cancer cases in the world occur in China. Among high-risk areas of esophageal squamous cell carcinoma (ESCC), Linxian County in Henan Province has the highest age-adjusted mortality rate of this cancer. 2 Epidemiological studies have revealed that the incidence of ESCC is associated with several factors, such as N-nitrosamines, which have been shown to be involved in the etiology of ESCC in Linxian. 3 However, studies in high-risk areas have demonstrated a strong tendency towards familial aggregation or clustering of cases within families, suggesting that genetic susceptibility factors may also play an important role in the etiology of ESCC.Previous studies have shown that several genetic abnormalities including amplification of C-myc, Int-2 and Hst, 4,5 mutation and/or deletion of p53 and Rb 2 and allelic deletion 6 have frequently occurred in human ESCC and esophageal cancer cell lines. However, the genetic events that lead to the development of esophageal cancer are not clear yet. In recent years, many studies of esophageal cancer are focused on the cloning and identification of novel esophageal cancer-related genes, which might play an important role in the carcinogenesis and development of the cancer. [7][8][9] Recently, we have cloned and identified a novel ESCC-related gene, ECRG2 (Genbank Accession Number AF 268198), from human normal esophageal epithelia. Firstly, we obtained an EST fragment by mRNA differential display techniques from 3 normal esophageal epithelia and 2 primary ESCC tissues from high incidence families in Linxian County and named it ECRG2. The RT-PCR detection results demonstrated that the expression of ECRG2 was down-regulated in ESCC as well as colon and brain tumors. 10 Secondly, we obtained the 569 bp full-length cDNA of the ECRG2 gene by SMARTTM RACE technique. We found that the gene contains 4 exons, spans about 3,540 bp on chromosome 5q32-33 and has a 258 bp open reading frame encoding an 85-amino acids polypeptide. 11 Analysis by bioinformatics has shown that 97% of the amino acid sequences of ECRG2 are homologous to a tumor associated KAZAL-type serine protease inhibitor that may play a central role in the protection of esophageal mucosa. 12 Thirdly, we studied the function of the ECRG2 gene by yeast 2-hybrid system and identified that the ECRG2 gene interacts directly ...

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“…Since this multiplex reaction produces nonoverlapping PCR products [3], it can also be electrophoresed in environments which do only allow low-cost silver staining instead of semiautomatic fragment length analysis. The triplex system has an exclusion chance of 1:2 X lo3 to 1:7 X lo6 and was incorporated into medico-legal DNA analysis by a number of forensic institutes and criminal investigation agencies.…”

Section: Short Tandem Repeat (Str) Locus Humdss306 In a Large Populatmentioning

confidence: 99%

Short tandem repeat (STR) locus HUMD8S306 in a large population sample from Germany

Benecke

Knopf²,

Voll³

et al. 1998

Electrophoresis

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Applied DNA typing in medico-legal investigations, in criminalistic practice, and in paternity cases often relies on high inclusion and exclusion probabilities. For that reason, the short autosomal tandem repeat locus D8D306 was validated for forensic use and incorporated into a nonoverlapping multiplex reaction with HUMDHFRP2 and HUMCD4: The allele frequencies of D8S306 in four different regions of Germany (n = 1220 alleles) were determined for use in a population database; the allele distributions did not significantly deviate from each other. The hererozygosity of D8S306 is 83%, expected exclusion chance in stain cases is 96% (paternity cases: 69%), the lowest amount of successfully amplified DNA was 30 pg. The alleles are in Hardy-Weinberg equilibrium.

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Five cases of forensic short tandem repeat DNA typing

Cited by 15 publications

References 35 publications

Haplotype Counting by Next-Generation Sequencing for Ultrasensitive Human DNA Detection

Haplotype Counting by Next-Generation Sequencing for Ultrasensitive Human DNA Detection

Short tandem repeat polymorphism in a novel esophageal cancer‐related gene (ECRG2) implicates susceptibility to esophageal cancer in Chinese population

Short tandem repeat (STR) locus HUMD8S306 in a large population sample from Germany

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