mtGenome resolution of the two most common Romanian haplotypes R0 and X2e1b and evaluation of point heteroplasmy detection by massively parallel sequencing

Turchi C, Stanciu F, Buscemi L, Tagliabracci A, „mte resolution of the two most common Romanian haplotypes R0 and X2e1b and evaluation of detection by massively parallel ”, Poster at Haploid Markers 2016 – Update on DNA variation, 10th International Y Chromosome workshop • 7th International EMPOP meeting. Berlin, May 20-21, 2016.

Abstract:

In the last years has been largely demonstrated that massively parallel technologies (MPS) offers new possibilities for , both for the more information that may be obtained in a single experiment from unique samples by analyzing combinations of s, both for the analytical cost-effectiveness. In particular, the full e (mte) using MPS has largely applied in the forensic context, as the throughput and sensitivity of the technology resulting in far more efficient data production than can be achieved via Sanger . Massively parallel of entire mte increases the power of discrimination, allows more comprehensive heteroplasmy detection, as well as high phylotic resolution, with respect to sequence information recovered from the solely control region (CR). Considering this limited range, some samples share identical haplotypes, especially the most frequent mt CR types that are typical of different populations. In an original dataset of 407 Romanian sequences (Turchi C. et al, in press), collected from the ral population belonging to four major historical regions Moldavia, , Wallachia and Dobruja, we observed 277 (68%) distinct haplotypes of which 220 (79%) were unique. The most common haplotype 16519C, 263G, 315.1C, ( R0) was shared by twenty-five individuals (6%), while the second most common haplotype 16126C, 16189A, 16223T, 16278T, 16519C, 73G, 195C, 263G, 315.1C ( X2e1b) was shared by ten individuals (4%). In order to investigate the degree of variation inside these two clades, twenty-one samples were submitted to entire mte using the Personal e Machine (PGM). In the same dataset, point heteroplasmic positions were observed at nine different sites (152Y, 185R, 214R, 225R, 235R, 16093Y, 16172Y, 16189Y and 16399R) in fifteen different samples. The ability to identify and utilize the discrimination potential of heteroplasmy will significantly enhance the value of mt analysis in forensic casework, but at present this condition is commonly disregarded mostly due to the poor sensitivity of the Sanger in detecting low-level heteroplasmy. Several studies have been carried out recently regarding the threshold for heteroplasmy detection by MPS, being rally suggested that this methodology is more sensitive and accurate. To investigate the level of and estimate alleles quantification, fifteen samples showing PHP in the control region were submitted to mte and the sequences obtained through the PGM are compared to those obtained by Sanger to determine heteroplasmy detection threshold with both technologies.

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3 comentarii la „mtGenome resolution of the two most common Romanian haplotypes R0 and X2e1b and evaluation of point heteroplasmy detection by massively parallel sequencing”

  1. Este o eroare la procentele pentru X2e1b sau la numarului de posesori ai haplogrupului din cei 407 ?
    Cu datele acestea pentru X2e1b procentul ar trebui sa fie de 2,46%.

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    • Într-adevăr este o eroare la numărul de posesori ai haplogrupului (17 în loc de 10).
      Eroarea fost a corectată în raportarea rezultatelor finale – Turchi C, Stanciu F, Paselli G, Buscemi L, Parson W, Tagliabracci A. The mitochondrial DNA makeup of Romanians: A forensic mtDNA control region database and phylogenetic characterization. Forensic Science International: Genetics. 2016;24:136-142.

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