Probabilistic SNP genotyping at low DNA concentrations

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Standard

Probabilistic SNP genotyping at low DNA concentrations. / Nielsen, M. B.; Andersen, M. M.; Eriksen, P. S.; Mogensen, H. S.; Morling, N.

I: Forensic Science International: Genetics Supplement Series, Bind 8, 2022, s. 151-152.

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt

Harvard

Nielsen, MB, Andersen, MM, Eriksen, PS, Mogensen, HS & Morling, N 2022, 'Probabilistic SNP genotyping at low DNA concentrations', Forensic Science International: Genetics Supplement Series, bind 8, s. 151-152. https://doi.org/10.1016/j.fsigss.2022.10.017

APA

Nielsen, M. B., Andersen, M. M., Eriksen, P. S., Mogensen, H. S., & Morling, N. (2022). Probabilistic SNP genotyping at low DNA concentrations. Forensic Science International: Genetics Supplement Series, 8, 151-152. https://doi.org/10.1016/j.fsigss.2022.10.017

Vancouver

Nielsen MB, Andersen MM, Eriksen PS, Mogensen HS, Morling N. Probabilistic SNP genotyping at low DNA concentrations. Forensic Science International: Genetics Supplement Series. 2022;8:151-152. https://doi.org/10.1016/j.fsigss.2022.10.017

Author

Nielsen, M. B. ; Andersen, M. M. ; Eriksen, P. S. ; Mogensen, H. S. ; Morling, N. / Probabilistic SNP genotyping at low DNA concentrations. I: Forensic Science International: Genetics Supplement Series. 2022 ; Bind 8. s. 151-152.

Bibtex

@article{de836ded6a16455f97d006b3c85ad1ca,
title = "Probabilistic SNP genotyping at low DNA concentrations",
abstract = "We present a statistical method for biallelic SNP genotyping that reduces the risk of wrong SNP calls and gives fewer no-calls. The method uses a symmetric multinomial logistic regression model with an intuitive graphical interpretation. Its probabilistic nature gives the user control over the accepted risk through the estimated genotype probabilities. We compared the performance of our method with the HID SNP Genotyper v.4.3.1 plug-in (HSG) (Thermo Fisher Scientific) and the additional criteria of the University of Copenhagen (UCPH) through a series of six DNA dilutions from 500 pg to 16 pg DNA. The HSG method made wrong calls from 62.5 pg DNA and below, while the UCPH method made wrong calls at 16 pg DNA. Our method allowed SNP genotyping of 16 pg DNA without making wrong calls. Depending on the DNA dilution, our method also reduced the number of no-calls by 70–96 % compared to UCPH method and 59–69 % compared to the HSG method. Our method can be used for any biallelic genotyping.",
keywords = "AIMs, Biallelic markers, HID SNP Genotyper, Low DNA concentrations, Massively parallel sequencing, Multinomial logistic regression",
author = "Nielsen, {M. B.} and Andersen, {M. M.} and Eriksen, {P. S.} and Mogensen, {H. S.} and N. Morling",
note = "Publisher Copyright: {\textcopyright} 2022 Elsevier B.V.",
year = "2022",
doi = "10.1016/j.fsigss.2022.10.017",
language = "English",
volume = "8",
pages = "151--152",
journal = "Forensic Science International: Genetics. Supplement Series",
issn = "1875-1768",
publisher = "Elsevier Ireland Ltd",

}

RIS

TY - JOUR

T1 - Probabilistic SNP genotyping at low DNA concentrations

AU - Nielsen, M. B.

AU - Andersen, M. M.

AU - Eriksen, P. S.

AU - Mogensen, H. S.

AU - Morling, N.

N1 - Publisher Copyright: © 2022 Elsevier B.V.

PY - 2022

Y1 - 2022

N2 - We present a statistical method for biallelic SNP genotyping that reduces the risk of wrong SNP calls and gives fewer no-calls. The method uses a symmetric multinomial logistic regression model with an intuitive graphical interpretation. Its probabilistic nature gives the user control over the accepted risk through the estimated genotype probabilities. We compared the performance of our method with the HID SNP Genotyper v.4.3.1 plug-in (HSG) (Thermo Fisher Scientific) and the additional criteria of the University of Copenhagen (UCPH) through a series of six DNA dilutions from 500 pg to 16 pg DNA. The HSG method made wrong calls from 62.5 pg DNA and below, while the UCPH method made wrong calls at 16 pg DNA. Our method allowed SNP genotyping of 16 pg DNA without making wrong calls. Depending on the DNA dilution, our method also reduced the number of no-calls by 70–96 % compared to UCPH method and 59–69 % compared to the HSG method. Our method can be used for any biallelic genotyping.

AB - We present a statistical method for biallelic SNP genotyping that reduces the risk of wrong SNP calls and gives fewer no-calls. The method uses a symmetric multinomial logistic regression model with an intuitive graphical interpretation. Its probabilistic nature gives the user control over the accepted risk through the estimated genotype probabilities. We compared the performance of our method with the HID SNP Genotyper v.4.3.1 plug-in (HSG) (Thermo Fisher Scientific) and the additional criteria of the University of Copenhagen (UCPH) through a series of six DNA dilutions from 500 pg to 16 pg DNA. The HSG method made wrong calls from 62.5 pg DNA and below, while the UCPH method made wrong calls at 16 pg DNA. Our method allowed SNP genotyping of 16 pg DNA without making wrong calls. Depending on the DNA dilution, our method also reduced the number of no-calls by 70–96 % compared to UCPH method and 59–69 % compared to the HSG method. Our method can be used for any biallelic genotyping.

KW - AIMs

KW - Biallelic markers

KW - HID SNP Genotyper

KW - Low DNA concentrations

KW - Massively parallel sequencing

KW - Multinomial logistic regression

U2 - 10.1016/j.fsigss.2022.10.017

DO - 10.1016/j.fsigss.2022.10.017

M3 - Journal article

AN - SCOPUS:85144245711

VL - 8

SP - 151

EP - 152

JO - Forensic Science International: Genetics. Supplement Series

JF - Forensic Science International: Genetics. Supplement Series

SN - 1875-1768

ER -

ID: 330780392