Inherited and De Novo Variation in Lithuanian Genomes: Introduction to the Analysis of the Generational Shift
Most genetic variants are rare and specific to the population, highlighting the importance of characterizing local population genetic diversity. Many countries have initiated population-based whole-genome sequencing (WGS) studies. Genomic variation within Lithuanian families are not available in the...
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MDPI AG
2022-03-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/13/4/569 |
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| author | Alina Urnikyte Laura Pranckeniene Ingrida Domarkiene Svetlana Dauengauer-Kirliene Alma Molyte Ausra Matuleviciene Ingrida Pilypiene Vaidutis Kučinskas |
| author_facet | Alina Urnikyte Laura Pranckeniene Ingrida Domarkiene Svetlana Dauengauer-Kirliene Alma Molyte Ausra Matuleviciene Ingrida Pilypiene Vaidutis Kučinskas |
| author_sort | Alina Urnikyte |
| collection | DOAJ |
| description | Most genetic variants are rare and specific to the population, highlighting the importance of characterizing local population genetic diversity. Many countries have initiated population-based whole-genome sequencing (WGS) studies. Genomic variation within Lithuanian families are not available in the public databases. Here, we describe initial findings of a high-coverage (an average of 36.27×) whole genome sequencing for 25 trios of the Lithuanian population. Each genome on average carried approximately 4,701,473 (±28,255) variants, where 80.6% (3,787,626) were single nucleotide polymorphisms (SNPs), and the rest 19.4% were indels. An average of 12.45% was novel according to dbSNP (build 150). The WGS structural variation (SV) analysis identified on average 9133 (±85.10) SVs, of which 95.85% were novel. De novo single nucleotide variation (SNV) analysis identified 4417 variants, where 1.1% de novo SNVs were exonic, 43.9% intronic, 51.9% intergenic, and the rest 3.13% in UTR or downstream sequence. Three potential pathogenic de novo variants in the <i>ZSWIM8</i>, <i>CDC42EP1</i>, and <i>RELA</i> genes were identified. Our findings provide useful information on local human population genomic variation, especially for de novo variants, and will be a valuable resource for further genetic studies, and medical implications. |
| first_indexed | 2024-03-09T10:35:55Z |
| format | Article |
| id | doaj.art-24bef9c3a9174da78986d72c4dddce9b |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-09T10:35:55Z |
| publishDate | 2022-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-24bef9c3a9174da78986d72c4dddce9b2023-12-01T20:56:20ZengMDPI AGGenes2073-44252022-03-0113456910.3390/genes13040569Inherited and De Novo Variation in Lithuanian Genomes: Introduction to the Analysis of the Generational ShiftAlina Urnikyte0Laura Pranckeniene1Ingrida Domarkiene2Svetlana Dauengauer-Kirliene3Alma Molyte4Ausra Matuleviciene5Ingrida Pilypiene6Vaidutis Kučinskas7Department of Human and Medical Genetics, Biomedical Science Institute, Faculty of Medicine, Vilnius University, Santariskiu Street 2, LT-08661 Vilnius, LithuaniaDepartment of Human and Medical Genetics, Biomedical Science Institute, Faculty of Medicine, Vilnius University, Santariskiu Street 2, LT-08661 Vilnius, LithuaniaDepartment of Human and Medical Genetics, Biomedical Science Institute, Faculty of Medicine, Vilnius University, Santariskiu Street 2, LT-08661 Vilnius, LithuaniaDepartment of Human and Medical Genetics, Biomedical Science Institute, Faculty of Medicine, Vilnius University, Santariskiu Street 2, LT-08661 Vilnius, LithuaniaDepartment of Human and Medical Genetics, Biomedical Science Institute, Faculty of Medicine, Vilnius University, Santariskiu Street 2, LT-08661 Vilnius, LithuaniaDepartment of Human and Medical Genetics, Biomedical Science Institute, Faculty of Medicine, Vilnius University, Santariskiu Street 2, LT-08661 Vilnius, LithuaniaDepartment of Human and Medical Genetics, Biomedical Science Institute, Faculty of Medicine, Vilnius University, Santariskiu Street 2, LT-08661 Vilnius, LithuaniaDepartment of Human and Medical Genetics, Biomedical Science Institute, Faculty of Medicine, Vilnius University, Santariskiu Street 2, LT-08661 Vilnius, LithuaniaMost genetic variants are rare and specific to the population, highlighting the importance of characterizing local population genetic diversity. Many countries have initiated population-based whole-genome sequencing (WGS) studies. Genomic variation within Lithuanian families are not available in the public databases. Here, we describe initial findings of a high-coverage (an average of 36.27×) whole genome sequencing for 25 trios of the Lithuanian population. Each genome on average carried approximately 4,701,473 (±28,255) variants, where 80.6% (3,787,626) were single nucleotide polymorphisms (SNPs), and the rest 19.4% were indels. An average of 12.45% was novel according to dbSNP (build 150). The WGS structural variation (SV) analysis identified on average 9133 (±85.10) SVs, of which 95.85% were novel. De novo single nucleotide variation (SNV) analysis identified 4417 variants, where 1.1% de novo SNVs were exonic, 43.9% intronic, 51.9% intergenic, and the rest 3.13% in UTR or downstream sequence. Three potential pathogenic de novo variants in the <i>ZSWIM8</i>, <i>CDC42EP1</i>, and <i>RELA</i> genes were identified. Our findings provide useful information on local human population genomic variation, especially for de novo variants, and will be a valuable resource for further genetic studies, and medical implications.https://www.mdpi.com/2073-4425/13/4/569whole genome sequencingSNVde novo variationnewbornstrios |
| spellingShingle | Alina Urnikyte Laura Pranckeniene Ingrida Domarkiene Svetlana Dauengauer-Kirliene Alma Molyte Ausra Matuleviciene Ingrida Pilypiene Vaidutis Kučinskas Inherited and De Novo Variation in Lithuanian Genomes: Introduction to the Analysis of the Generational Shift Genes whole genome sequencing SNV de novo variation newborns trios |
| title | Inherited and De Novo Variation in Lithuanian Genomes: Introduction to the Analysis of the Generational Shift |
| title_full | Inherited and De Novo Variation in Lithuanian Genomes: Introduction to the Analysis of the Generational Shift |
| title_fullStr | Inherited and De Novo Variation in Lithuanian Genomes: Introduction to the Analysis of the Generational Shift |
| title_full_unstemmed | Inherited and De Novo Variation in Lithuanian Genomes: Introduction to the Analysis of the Generational Shift |
| title_short | Inherited and De Novo Variation in Lithuanian Genomes: Introduction to the Analysis of the Generational Shift |
| title_sort | inherited and de novo variation in lithuanian genomes introduction to the analysis of the generational shift |
| topic | whole genome sequencing SNV de novo variation newborns trios |
| url | https://www.mdpi.com/2073-4425/13/4/569 |
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