Stutter analysis of complex STR MPS data
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Stutter analysis of complex STR MPS data. / Vilsen, Søren B.; Tvedebrink, Torben; Eriksen, Poul Svante; Bøsting, Claus; Hussing, Christian; Mogensen, Helle Smidt; Morling, Niels.
I: Forensic Science International: Genetics, Bind 35, 01.07.2018, s. 107-112.Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
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TY - JOUR
T1 - Stutter analysis of complex STR MPS data
AU - Vilsen, Søren B.
AU - Tvedebrink, Torben
AU - Eriksen, Poul Svante
AU - Bøsting, Claus
AU - Hussing, Christian
AU - Mogensen, Helle Smidt
AU - Morling, Niels
PY - 2018/7/1
Y1 - 2018/7/1
N2 - Stutters are common and well documented artefacts of amplification of short tandem repeat (STR) regions when using polymerase chain reaction (PCR) occurring as strands one or more motifs shorter or longer than the parental allele. Understanding the mechanism and rate by which stutters are created is especially important when the samples contain small amounts of DNA or DNA from multiple contributors. It has been shown that there is a linear relationship between the longest uninterrupted stretch (LUS) and the stutter ratio. This holds if there is only a single type of stutter variant. However, with massively parallel sequencing (MPS), we see that alleles may create different stutters corresponding to stuttering of different parts of the parental allele. This calls for a refinement of the LUS concept. We analysed all uninterrupted stretches, here called blocks, and identified the block from which the stutter originated. We defined the block length of the missing motif (BLMM) as the length of the identified block. We found that the relationship between the stutter ratio and BLMM was linear using a simple system of recurrence relations. We found that the mean square error decreased by a factor up to 17.5 for compound and complex autosomal markers when using BLMM instead of LUS.
AB - Stutters are common and well documented artefacts of amplification of short tandem repeat (STR) regions when using polymerase chain reaction (PCR) occurring as strands one or more motifs shorter or longer than the parental allele. Understanding the mechanism and rate by which stutters are created is especially important when the samples contain small amounts of DNA or DNA from multiple contributors. It has been shown that there is a linear relationship between the longest uninterrupted stretch (LUS) and the stutter ratio. This holds if there is only a single type of stutter variant. However, with massively parallel sequencing (MPS), we see that alleles may create different stutters corresponding to stuttering of different parts of the parental allele. This calls for a refinement of the LUS concept. We analysed all uninterrupted stretches, here called blocks, and identified the block from which the stutter originated. We defined the block length of the missing motif (BLMM) as the length of the identified block. We found that the relationship between the stutter ratio and BLMM was linear using a simple system of recurrence relations. We found that the mean square error decreased by a factor up to 17.5 for compound and complex autosomal markers when using BLMM instead of LUS.
KW - BLMM
KW - Blocks
KW - LUS
KW - Missing motif
KW - MPS
KW - Stutter
UR - http://www.scopus.com/inward/record.url?scp=85046728350&partnerID=8YFLogxK
U2 - 10.1016/j.fsigen.2018.04.003
DO - 10.1016/j.fsigen.2018.04.003
M3 - Journal article
C2 - 29702330
AN - SCOPUS:85046728350
VL - 35
SP - 107
EP - 112
JO - Forensic Science International: Genetics
JF - Forensic Science International: Genetics
SN - 1872-4973
ER -
ID: 203553540