Identification of Pathogenic Variant Burden and Selection of Optimal Diagnostic Method Is a Way to Improve Carrier Screening for Autosomal Recessive Diseases

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Identification of Pathogenic Variant Burden and Selection of Optimal Diagnostic Method Is a Way to Improve Carrier Screening for Autosomal Recessive Diseases. / Sotnikova, Evgeniia A.; Kiseleva, Anna V.; Kutsenko, Vladimir A. et al.

In: Journal of Personalized Medicine, Vol. 12, No. 7, 1132, 07.2022.

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

Harvard

Sotnikova, EA, Kiseleva, AV, Kutsenko, VA, Zharikova, AA, Ramensky, VE, Divashuk, MG, Vyatkin, YV, Klimushina, MV, Ershova, AI, Revazyan, KZ, Skirko, OP, Zaicenoka, M, Efimova, IA, Pokrovskaya, MS, Kopylova, OV, Glechan, AM, Shalnova, SA, Meshkov, AN & Drapkina, OM 2022, 'Identification of Pathogenic Variant Burden and Selection of Optimal Diagnostic Method Is a Way to Improve Carrier Screening for Autosomal Recessive Diseases', Journal of Personalized Medicine, vol. 12, no. 7, 1132. https://doi.org/10.3390/jpm12071132

APA

Sotnikova, E. A., Kiseleva, A. V., Kutsenko, V. A., Zharikova, A. A., Ramensky, V. E., Divashuk, M. G., Vyatkin, Y. V., Klimushina, M. V., Ershova, A. I., Revazyan, K. Z., Skirko, O. P., Zaicenoka, M., Efimova, I. A., Pokrovskaya, M. S., Kopylova, O. V., Glechan, A. M., Shalnova, S. A., Meshkov, A. N., & Drapkina, O. M. (2022). Identification of Pathogenic Variant Burden and Selection of Optimal Diagnostic Method Is a Way to Improve Carrier Screening for Autosomal Recessive Diseases. Journal of Personalized Medicine, 12(7), [1132]. https://doi.org/10.3390/jpm12071132

Vancouver

Sotnikova EA, Kiseleva AV, Kutsenko VA, Zharikova AA, Ramensky VE, Divashuk MG et al. Identification of Pathogenic Variant Burden and Selection of Optimal Diagnostic Method Is a Way to Improve Carrier Screening for Autosomal Recessive Diseases. Journal of Personalized Medicine. 2022 Jul;12(7):1132. doi: 10.3390/jpm12071132

Author

Sotnikova, Evgeniia A. ; Kiseleva, Anna V. ; Kutsenko, Vladimir A. et al. / Identification of Pathogenic Variant Burden and Selection of Optimal Diagnostic Method Is a Way to Improve Carrier Screening for Autosomal Recessive Diseases. In: Journal of Personalized Medicine. 2022 ; Vol. 12, No. 7.

BibTeX

@article{2ac9b36af9f0476db06268e514aa21da,

title = "Identification of Pathogenic Variant Burden and Selection of Optimal Diagnostic Method Is a Way to Improve Carrier Screening for Autosomal Recessive Diseases",

abstract = "Cystic fibrosis, phenylketonuria, alpha-1 antitrypsin deficiency, and sensorineural hearing loss are among the most common autosomal recessive diseases, which require carrier screening. The evaluation of population allele frequencies (AF) of pathogenic variants in genes associated with these conditions and the choice of the best genotyping method are the necessary steps toward development and practical implementation of carrier-screening programs. We performed custom panel genotyping of 3821 unrelated participants from two Russian population representative samples and three patient groups using real-time polymerase chain reaction (PCR) and next generation sequencing (NGS). The custom panel included 115 known pathogenic variants in the CFTR, PAH, SERPINA1, and GJB2 genes. Overall, 38 variants were detected. The comparison of genotyping platforms revealed the following advantages of real-time PCR: relatively low cost, simple genotyping data analysis, and easier detection of large indels, while NGS showed better accuracy of variants identification and capability for detection of additional pathogenic variants in adjacent regions. A total of 23 variants had significant differences in estimated AF comparing with non-Finnish Europeans from gnomAD. This study provides new AF data for variants associated with the studied disorders and the comparison of genotyping methods for carrier screening.",

keywords = "allele frequency, autosomal recessive disorders, carrier screening, CFTR, GJB2, PAH, population, SERPINA1",

author = "Sotnikova, {Evgeniia A.} and Kiseleva, {Anna V.} and Kutsenko, {Vladimir A.} and Zharikova, {Anastasia A.} and Ramensky, {Vasily E.} and Divashuk, {Mikhail G.} and Vyatkin, {Yuri V.} and Klimushina, {Marina V.} and Ershova, {Alexandra I.} and Revazyan, {Karina Z.} and Skirko, {Olga P.} and Marija Zaicenoka and Efimova, {Irina A.} and Pokrovskaya, {Maria S.} and Kopylova, {Oksana V.} and Glechan, {Anush M.} and Shalnova, {Svetlana A.} and Meshkov, {Alexey N.} and Drapkina, {Oxana M.}",

note = "Funding Information: This study was supported by the RFBR and DFG joint research project no 20-54-12008. Publisher Copyright: {\textcopyright} 2022 by the authors.",

year = "2022",

month = jul,

doi = "10.3390/jpm12071132",

language = "English",

volume = "12",

journal = "Journal of Personalized Medicine",

issn = "2075-4426",

publisher = "Multidisciplinary Digital Publishing Institute (MDPI)",

number = "7",

}

RIS

TY - JOUR

T1 - Identification of Pathogenic Variant Burden and Selection of Optimal Diagnostic Method Is a Way to Improve Carrier Screening for Autosomal Recessive Diseases

AU - Sotnikova, Evgeniia A.

AU - Kiseleva, Anna V.

AU - Kutsenko, Vladimir A.

AU - Zharikova, Anastasia A.

AU - Ramensky, Vasily E.

AU - Divashuk, Mikhail G.

AU - Vyatkin, Yuri V.

AU - Klimushina, Marina V.

AU - Ershova, Alexandra I.

AU - Revazyan, Karina Z.

AU - Skirko, Olga P.

AU - Zaicenoka, Marija

AU - Efimova, Irina A.

AU - Pokrovskaya, Maria S.

AU - Kopylova, Oksana V.

AU - Glechan, Anush M.

AU - Shalnova, Svetlana A.

AU - Meshkov, Alexey N.

AU - Drapkina, Oxana M.

PY - 2022/7

Y1 - 2022/7

N2 - Cystic fibrosis, phenylketonuria, alpha-1 antitrypsin deficiency, and sensorineural hearing loss are among the most common autosomal recessive diseases, which require carrier screening. The evaluation of population allele frequencies (AF) of pathogenic variants in genes associated with these conditions and the choice of the best genotyping method are the necessary steps toward development and practical implementation of carrier-screening programs. We performed custom panel genotyping of 3821 unrelated participants from two Russian population representative samples and three patient groups using real-time polymerase chain reaction (PCR) and next generation sequencing (NGS). The custom panel included 115 known pathogenic variants in the CFTR, PAH, SERPINA1, and GJB2 genes. Overall, 38 variants were detected. The comparison of genotyping platforms revealed the following advantages of real-time PCR: relatively low cost, simple genotyping data analysis, and easier detection of large indels, while NGS showed better accuracy of variants identification and capability for detection of additional pathogenic variants in adjacent regions. A total of 23 variants had significant differences in estimated AF comparing with non-Finnish Europeans from gnomAD. This study provides new AF data for variants associated with the studied disorders and the comparison of genotyping methods for carrier screening.

AB - Cystic fibrosis, phenylketonuria, alpha-1 antitrypsin deficiency, and sensorineural hearing loss are among the most common autosomal recessive diseases, which require carrier screening. The evaluation of population allele frequencies (AF) of pathogenic variants in genes associated with these conditions and the choice of the best genotyping method are the necessary steps toward development and practical implementation of carrier-screening programs. We performed custom panel genotyping of 3821 unrelated participants from two Russian population representative samples and three patient groups using real-time polymerase chain reaction (PCR) and next generation sequencing (NGS). The custom panel included 115 known pathogenic variants in the CFTR, PAH, SERPINA1, and GJB2 genes. Overall, 38 variants were detected. The comparison of genotyping platforms revealed the following advantages of real-time PCR: relatively low cost, simple genotyping data analysis, and easier detection of large indels, while NGS showed better accuracy of variants identification and capability for detection of additional pathogenic variants in adjacent regions. A total of 23 variants had significant differences in estimated AF comparing with non-Finnish Europeans from gnomAD. This study provides new AF data for variants associated with the studied disorders and the comparison of genotyping methods for carrier screening.

KW - allele frequency

KW - autosomal recessive disorders

KW - carrier screening

KW - CFTR

KW - GJB2

KW - PAH

KW - population

KW - SERPINA1

UR - http://www.scopus.com/inward/record.url?scp=85136208641&partnerID=8YFLogxK

UR - https://www.elibrary.ru/item.asp?id=49050112

UR - https://www.mendeley.com/catalogue/8d07bd58-25f1-3b38-a80f-870407c418ad/

U2 - 10.3390/jpm12071132

DO - 10.3390/jpm12071132

M3 - Article

C2 - 35887629

AN - SCOPUS:85136208641

VL - 12

JO - Journal of Personalized Medicine

JF - Journal of Personalized Medicine

SN - 2075-4426

IS - 7

M1 - 1132

ER -

ID: 36958311