DIP-microhaplotypes: new markers for detection of unbalanced DNA mixtures
- 5 May 2020
- journal article
- research article
- Published by Springer Science and Business Media LLC in International journal of legal medicine
- Vol. 135 (1), 13-21
- https://doi.org/10.1007/s00414-020-02288-y
Abstract
The identification of a suspect in a degraded and unbalanced DNA mixture has been a challenge for the standard short tandem repeat polymorphisms (STR) typing. Several methods have been introduced to solve this problem, such as DIP-STR, DIP-SNP, and SNP-STR markers. In this study, we proposed DIP-microhaplotype (deletion/insertion linked a chain of SNPs) as a kind of new genetic marker to type the unbalanced and degraded DNA mixture. We established the detection method with ten DIP-microhaplotype markers including 26 SNPs using allele-specific multiplex PCR followed by SNaPshot assay. This novel compound marker allows us to detect the minor DNA with a sensitivity of 1:100 to 1:1000 in a DNA mixture of any gender. Most of the DIP-microhaplotype markers had a relatively high probability of informative alleles with an average informative value (I value) of 0.308. In all, we proposed DIP-microhaplotype as a novel type of DNA marker for the detection of minor contributor from unbalanced DNA mixtures. Due to their inherent shorter length, higher polymorphism, and sensitivity, DIP-microhaplotypes are promising markers for the examination of the degraded and unbalanced mixtures in forensic stains or clinical chimeras.Keywords
Funding Information
- National Natural Science Foundation of China (30900593, 81701868)
- the Natural Science Foundation of Shanxi Province, China (201601D011091)
- Shanxi Provincial Key Research and Development Project (201803D31069)
This publication has 34 references indexed in Scilit:
- Technical note: developmental validation of a novel 6-dye typing system with 36 Y-STR lociInternational journal of legal medicine, 2018
- Non-invasive prenatal paternity testing using cell-free fetal DNA from maternal plasma: DNA isolation and genetic marker studiesLegal Medicine, 2018
- Producing standard damaged DNA samples by heating: pitfalls and suggestionsAnalytical Biochemistry, 2018
- A preliminary evaluation study of new generation multiplex STR kits comprising of the CODIS core loci and the European Standard Set lociJournal of Forensic and Legal Medicine, 2017
- Early genetic aberrations in patients with sporadic colorectal cancerMolecular Carcinogenesis, 2017
- Identification of potential mutations and genomic alterations in the epithelial and spindle cell components of biphasic synovial sarcomas using a human exome SNP chipBMC Medical Genomics, 2015
- Whole genome amplification of degraded and nondegraded DNA for forensic purposesInternational journal of legal medicine, 2012
- Developmental Validation of the AmpFℓSTR® Identifiler® Plus PCR Amplification Kit: An Established Multiplex Assay with Improved PerformanceJournal of Forensic Sciences, 2011
- Y chromosome STR typing in crime caseworkForensic Science, Medicine and Pathology, 2009
- DNA commission of the International Society of Forensic Genetics: Recommendations on the interpretation of mixturesForensic Science International, 2006