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Pilot screening of cell-free mtdna in nipt : Quality control, variant calling, and haplogroup determination. / Morshneva, Alisa; Kozyulina, Polina; Vashukova, Elena; Tarasenko, Olga; Dvoynova, Natalia; Chentsova, Anastasia; Talantova, Olga; Koroteev, Alexander; Ivanov, Dmitrii; Serebryakova, Elena; Ivashchenko, Tatyana; Sukhomyasova, Aitalina; Maksimova, Nadezhda; Bespalova, Olesya; Kogan, Igor; Baranov, Vladislav; Glotov, Andrey.

In: Genes, Vol. 12, No. 5, 743, 05.2021.

Research output: Contribution to journal › Article › peer-review

Harvard

Morshneva, A, Kozyulina, P, Vashukova, E, Tarasenko, O, Dvoynova, N, Chentsova, A, Talantova, O, Koroteev, A, Ivanov, D, Serebryakova, E, Ivashchenko, T, Sukhomyasova, A, Maksimova, N, Bespalova, O, Kogan, I, Baranov, V & Glotov, A 2021, 'Pilot screening of cell-free mtdna in nipt: Quality control, variant calling, and haplogroup determination', Genes, vol. 12, no. 5, 743. https://doi.org/10.3390/genes12050743

APA

Morshneva, A., Kozyulina, P., Vashukova, E., Tarasenko, O., Dvoynova, N., Chentsova, A., Talantova, O., Koroteev, A., Ivanov, D., Serebryakova, E., Ivashchenko, T., Sukhomyasova, A., Maksimova, N., Bespalova, O., Kogan, I., Baranov, V., & Glotov, A. (2021). Pilot screening of cell-free mtdna in nipt: Quality control, variant calling, and haplogroup determination. Genes, 12(5), [743]. https://doi.org/10.3390/genes12050743

Vancouver

Morshneva A, Kozyulina P, Vashukova E, Tarasenko O, Dvoynova N, Chentsova A et al. Pilot screening of cell-free mtdna in nipt: Quality control, variant calling, and haplogroup determination. Genes. 2021 May;12(5). 743. https://doi.org/10.3390/genes12050743

Author

Morshneva, Alisa ; Kozyulina, Polina ; Vashukova, Elena ; Tarasenko, Olga ; Dvoynova, Natalia ; Chentsova, Anastasia ; Talantova, Olga ; Koroteev, Alexander ; Ivanov, Dmitrii ; Serebryakova, Elena ; Ivashchenko, Tatyana ; Sukhomyasova, Aitalina ; Maksimova, Nadezhda ; Bespalova, Olesya ; Kogan, Igor ; Baranov, Vladislav ; Glotov, Andrey. / Pilot screening of cell-free mtdna in nipt : Quality control, variant calling, and haplogroup determination. In: Genes. 2021 ; Vol. 12, No. 5.

BibTeX

@article{a213506cee7748e3b026ee4f1682f2e3,
title = "Pilot screening of cell-free mtdna in nipt: Quality control, variant calling, and haplogroup determination",
abstract = "Clinical tests based on whole-genome sequencing are generally focused on a single task approach, testing one or several parameters, although whole-genome sequencing (WGS) provides us with large data sets that can be used for many supportive analyses. In spite of low genome cov-erage, data of WGS-based non-invasive prenatal testing (NIPT) contain fully sequenced mitochon-drial DNA (mtDNA). This mtDNA can be used for variant calling, ancestry analysis, population studies and other approaches that extend NIPT functionality. In this study, we analyse mtDNA pool from 645 cell-free DNA (cfDNA) samples of pregnant women from different regions of Russia, ex-plore the effects of transportation and storing conditions on mtDNA content, analyse effects, frequency and location of mitochondrial variants called from samples and perform haplogroup anal-ysis, revealing the most common mitochondrial superclades. We have shown that, despite the rela-tively low sequencing depth of unamplified mtDNA from cfDNA samples, the mtDNA analysis in these samples is still an informative instrument suitable for research and screening purposes.",
keywords = "Breast cancer, CfDNA, ClinVar, Foetal fraction, Mitochondrial diseases, Mitochondrial variants, MtDNA, MtDNA haplogroups, NIPT, Population studies, SNPs, Transportation, DNA, Mitochondrial/genetics, Humans, Haplotypes/genetics, Russia, Polymorphism, Single Nucleotide/genetics, Female, Whole Genome Sequencing/methods, Noninvasive Prenatal Testing/methods, Quality Control, Cell-Free Nucleic Acids/genetics, Pregnancy, Pilot Projects, Mitochondria/genetics, mtDNA haplogroups, SET, mtDNA, ORIGIN, mitochondrial diseases, PLASMA, cfDNA, MUTATIONS, mitochondrial variants, INCREASES, breast cancer, FETAL DNA, MITOCHONDRIAL-DNA, ANCESTRY, population studies, DAMAGE, REGION, transportation, foetal fraction",
author = "Alisa Morshneva and Polina Kozyulina and Elena Vashukova and Olga Tarasenko and Natalia Dvoynova and Anastasia Chentsova and Olga Talantova and Alexander Koroteev and Dmitrii Ivanov and Elena Serebryakova and Tatyana Ivashchenko and Aitalina Sukhomyasova and Nadezhda Maksimova and Olesya Bespalova and Igor Kogan and Vladislav Baranov and Andrey Glotov",
note = "Publisher Copyright: {\textcopyright} 2021 by the authors. Licensee MDPI, Basel, Switzerland.",
year = "2021",
month = may,
doi = "10.3390/genes12050743",
language = "English",
volume = "12",
journal = "Genes",
issn = "2073-4425",
publisher = "MDPI AG",
number = "5",

}

RIS

TY - JOUR

T1 - Pilot screening of cell-free mtdna in nipt

T2 - Quality control, variant calling, and haplogroup determination

AU - Morshneva, Alisa

AU - Kozyulina, Polina

AU - Vashukova, Elena

AU - Tarasenko, Olga

AU - Dvoynova, Natalia

AU - Chentsova, Anastasia

AU - Talantova, Olga

AU - Koroteev, Alexander

AU - Ivanov, Dmitrii

AU - Serebryakova, Elena

AU - Ivashchenko, Tatyana

AU - Sukhomyasova, Aitalina

AU - Maksimova, Nadezhda

AU - Bespalova, Olesya

AU - Kogan, Igor

AU - Baranov, Vladislav

AU - Glotov, Andrey

N1 - Publisher Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland.

PY - 2021/5

Y1 - 2021/5

N2 - Clinical tests based on whole-genome sequencing are generally focused on a single task approach, testing one or several parameters, although whole-genome sequencing (WGS) provides us with large data sets that can be used for many supportive analyses. In spite of low genome cov-erage, data of WGS-based non-invasive prenatal testing (NIPT) contain fully sequenced mitochon-drial DNA (mtDNA). This mtDNA can be used for variant calling, ancestry analysis, population studies and other approaches that extend NIPT functionality. In this study, we analyse mtDNA pool from 645 cell-free DNA (cfDNA) samples of pregnant women from different regions of Russia, ex-plore the effects of transportation and storing conditions on mtDNA content, analyse effects, frequency and location of mitochondrial variants called from samples and perform haplogroup anal-ysis, revealing the most common mitochondrial superclades. We have shown that, despite the rela-tively low sequencing depth of unamplified mtDNA from cfDNA samples, the mtDNA analysis in these samples is still an informative instrument suitable for research and screening purposes.

AB - Clinical tests based on whole-genome sequencing are generally focused on a single task approach, testing one or several parameters, although whole-genome sequencing (WGS) provides us with large data sets that can be used for many supportive analyses. In spite of low genome cov-erage, data of WGS-based non-invasive prenatal testing (NIPT) contain fully sequenced mitochon-drial DNA (mtDNA). This mtDNA can be used for variant calling, ancestry analysis, population studies and other approaches that extend NIPT functionality. In this study, we analyse mtDNA pool from 645 cell-free DNA (cfDNA) samples of pregnant women from different regions of Russia, ex-plore the effects of transportation and storing conditions on mtDNA content, analyse effects, frequency and location of mitochondrial variants called from samples and perform haplogroup anal-ysis, revealing the most common mitochondrial superclades. We have shown that, despite the rela-tively low sequencing depth of unamplified mtDNA from cfDNA samples, the mtDNA analysis in these samples is still an informative instrument suitable for research and screening purposes.

KW - Breast cancer

KW - CfDNA

KW - ClinVar

KW - Foetal fraction

KW - Mitochondrial diseases

KW - Mitochondrial variants

KW - MtDNA

KW - MtDNA haplogroups

KW - NIPT

KW - Population studies

KW - SNPs

KW - Transportation

KW - DNA, Mitochondrial/genetics

KW - Humans

KW - Haplotypes/genetics

KW - Russia

KW - Polymorphism, Single Nucleotide/genetics

KW - Female

KW - Whole Genome Sequencing/methods

KW - Noninvasive Prenatal Testing/methods

KW - Quality Control

KW - Cell-Free Nucleic Acids/genetics

KW - Pregnancy

KW - Pilot Projects

KW - Mitochondria/genetics

KW - mtDNA haplogroups

KW - SET

KW - mtDNA

KW - ORIGIN

KW - mitochondrial diseases

KW - PLASMA

KW - cfDNA

KW - MUTATIONS

KW - mitochondrial variants

KW - INCREASES

KW - breast cancer

KW - FETAL DNA

KW - MITOCHONDRIAL-DNA

KW - ANCESTRY

KW - population studies

KW - DAMAGE

KW - REGION

KW - transportation

KW - foetal fraction

UR - http://www.scopus.com/inward/record.url?scp=85106934266&partnerID=8YFLogxK

UR - https://www.mendeley.com/catalogue/902601d9-a2c0-35f3-9f96-c882eba04f85/

U2 - 10.3390/genes12050743

DO - 10.3390/genes12050743

M3 - Article

C2 - 34069212

AN - SCOPUS:85106934266

VL - 12

JO - Genes

JF - Genes

SN - 2073-4425

IS - 5

M1 - 743

ER -

ID: 88552499