Analysis of artificially degraded DNA using STRs and SNPs—results of a collaborative European (EDNAP) exercise

Dixon, Lindsey; Dobbins, A.E.; Pulker, Hannah; Butler, John M.; Vallone, Peter M.; Coble, Michael D.; Parson, Walther; Berger, Burkhard; Grubwieser, Petra; Mogensen, Helle Smidt; Morling, Niels; Nielsen, Karsten; Sánchez, Juan José Martínez; Petkovski, Elizabet; Carracedo, Ángel; Sánchez-Diz, Paula; Ramos-Luis, Eva; Brión, Marı́a; Irwin, Jodi A.; Just, Rebecca S.; Loreille, Odile; Parsons, Thomas J.; Syndercombe‐Court, Denise; Schmitter, H.; Stradmann‐Bellinghausen, Beate; Bender, Klaus; Gill, Peter

doi:10.1016/j.forsciint.2005.11.011

Cited by 127 publications

(67 citation statements)

References 41 publications

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“…As with all polymerase chain reaction (PCR)-based methods, allele dropouts may pose a problem owing to low-quality DNA, and this might in turn falsely be interpreted as LOH. The problem of allele dropouts is, however, more pronounced when using microsatellite markers (Utsuno and Minaguchi, 2004;Petkovski et al, 2005;Dixon et al, 2006). Consequently, the use of SNP markers as well as careful DNA quantification and genotyping multiple parallel samples should ensure reliable estimates of LOH.…”

Section: Discussionmentioning

confidence: 99%

Mechanisms of inactivation of MLH1 in hereditary nonpolyposis colorectal carcinoma: a novel approach

et al. 2007

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Mutations in the DNA mismatch repair gene MLH1 are a major cause of hereditary nonpolyposis colorectal cancer (HNPCC). No mutant phenotype is observed before the wild-type (wt) allele is somatically inactivated in target tissue. We addressed the mechanisms of MLH1 inactivation in 25 colorectal (CRC) and 32 endometrial cancers (ECs) from MLH1 mutation carriers (Mut1, in-frame genomic deletion; Mut2, out-of-frame splice site mutation; Mut3, missense mutation). By a quantitative method, matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF), utilizing four intragenic single nucleotide polymorphisms and mutations, loss of heterozygosity (LOH) was present in 31/57 (54.4%) of tumors. The wt allele displayed LOH more often than the mutant allele (23/57 vs 8/57, P ¼ 0.006). For Mut1, LOH was more frequent in CRC than EC (10/11 vs 1/13, Po0.0001), whereas Mut2 and Mut3 displayed opposite LOH pattern. Moreover, although wt LOH predominated in CRC irrespective of the predisposing mutation, LOH often affected the mutant allele in EC from Mut2 and Mut3 carriers (6/19, 31.6%). MLH1 promoter methylation, which reflected a more widespread hypermethylation tendency, occurred in 4/55 (7.3%) of tumors and was inversely associated with LOH. In conclusion, the patterns of somatic events (LOH and promoter methylation) differ depending on the tissue and germline mutation, which may in part explain the differential tumor susceptibility of different organs in HNPCC. MALDI-TOF provides a novel approach for the detection and quantification of LOH.

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Section: Discussionmentioning

confidence: 99%

Mechanisms of inactivation of MLH1 in hereditary nonpolyposis colorectal carcinoma: a novel approach

et al. 2007

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“…In 2004, a collaborative study between nine European and US laboratories was organised under the auspices of the European DNA Profiling group (EDNAP) on the same sets of degraded samples. The results were collated and analysed and, in general, mini-STR systems were shown to be the most effective [26]. Since then, a number of other studies have demonstrated that successful analysis of degraded DNA specimens from mass disasters or compromised forensic evidence improves with smaller-sized PCR products [8,10,12,14,[27][28][29][30][31].…”

Section: History and Progressionmentioning

confidence: 99%

“…As reported in the literature, the amplicon size of a miniSTR is below 200bp, above which chances of getting a complete profile from a degraded sample diminish significantly [42]. Others have suggested that the optimum product size is below 150bp [26]. Only a handful of studies are available on ChrX miniSTRs which are often combined with other larger-amplicon size markers, hence making them unsuitable for use in degraded sample studies and casework.…”

Section: X-chromosomal Strs and Ministrs: Identity Testing And Beyondmentioning

confidence: 99%

Scope of X-Chromosomal MiniSTRs: Current Developments

Israr¹

2014

J Forensic

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The experience of using autosomal short-length amplicon STRs or miniSTRs in profiling of degraded DNA and mass disaster victims is extended into the realm of X-chromosomal (ChrX) STR miniaturization. About half of the total X-STRs are now short-length amplicons and the focus is shifting to using the mini versions of all of them. Joint multiplexing of these loci can be used for solving complex paternity cases and association of mass disaster victims with their families. This technology may herald a new dimension for research in population genetics and evolution. We present an overview of the progress made thus far and the future scope and prospects for X-miniSTRs.

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“…In addition, storage conditions are also important for DNA yield and quality, such as temperature and storage and transfer time. To avoid high temperature and long transfer times, the samples were refrigerated and frozen more carefully during transport and storage, which can prevent DNA degradation and bacteria growth (Dixon et al, 2006, Rogers et al, 2007. As reported, highquality DNA was obtained after transport at room temperature for 1 week and storage for 13-14 months at -70 ºC (London et al, 2001).…”

Section: Figurementioning

confidence: 99%

An Application of Salivary DNA in Twin Research of Chinese Children

Zhang

2008

Twin Res Hum Genet

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S ince saliva collection is noninvasive, painless and inexpensive, it may become an alternative to obtain genomic DNA, which is critical to evaluate zygosity and the role of genetic factors in twin research. This study provided a rough description of salivary DNA in Chinese twin children, and presented the DNA yield and quality extracted from saliva in a large-scale children sample, which supplied an example for saliva sample using in genetic epidemiology. Three milliliters of saliva was collected from 356 twin children aged 6 to 15, and DNA was extracted by a com mercial DNA isolation kit. The DNA yield and purity was determined by spectrophotometry at 260nm and 280nm. The zygosity determination of the same-sex twins and the assay of Polymerase Chain Reaction-Restriction Fragment Length Polymorphism indicated the quality of salivary DNA. The amount of extracted DNA from three milliliters of saliva was about 34.91µg (2.20 ~ 122.04µg), average OD 260/280 values was 1.84. Saliva DNA is a reliable sample for the determination of twins' zygosity. We conclude that saliva may be a feasible and reliable source of DNA for genetic epidemiology studies, especially for twin research.

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Analysis of artificially degraded DNA using STRs and SNPs—results of a collaborative European (EDNAP) exercise

Cited by 127 publications

References 41 publications

Mechanisms of inactivation of MLH1 in hereditary nonpolyposis colorectal carcinoma: a novel approach

Mechanisms of inactivation of MLH1 in hereditary nonpolyposis colorectal carcinoma: a novel approach

Scope of X-Chromosomal MiniSTRs: Current Developments

An Application of Salivary DNA in Twin Research of Chinese Children

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