Optimized detection of insertions/deletions (INDELs) in whole-exome sequencing data.
Insertion and deletion (INDEL) mutations, the most common type of structural variance, are associated with several human diseases. The detection of INDELs through next-generation sequencing (NGS) is becoming more common due to the decrease in costs, the increase in efficiency, and sensitivity improv...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2017-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC5549930?pdf=render |
| _version_ | 1819232295980105728 |
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| author | Bo-Young Kim Jung Hoon Park Hye-Yeong Jo Soo Kyung Koo Mi-Hyun Park |
| author_facet | Bo-Young Kim Jung Hoon Park Hye-Yeong Jo Soo Kyung Koo Mi-Hyun Park |
| author_sort | Bo-Young Kim |
| collection | DOAJ |
| description | Insertion and deletion (INDEL) mutations, the most common type of structural variance, are associated with several human diseases. The detection of INDELs through next-generation sequencing (NGS) is becoming more common due to the decrease in costs, the increase in efficiency, and sensitivity improvements demonstrated by the various sequencing platforms and analytical tools. However, there are still many errors associated with INDEL variant calling, and distinguishing INDELs from errors in NGS remains challenging. To evaluate INDEL calling from whole-exome sequencing (WES) data, we performed Sanger sequencing for all INDELs called from the several calling algorithm. We compared the performance of the four algorithms (i.e. GATK, SAMtools, Dindel, and Freebayes) for INDEL detection from the same sample. We examined the sensitivity and PPV of GATK (90.2 and 89.5%, respectively), SAMtools (75.3 and 94.4%, respectively), Dindel (90.1 and 88.6%, respectively), and Freebayes (80.1 and 94.4%, respectively). GATK had the highest sensitivity. Furthermore, we identified INDELs with high PPV (4 algorithms intersection: 98.7%, 3 algorithms intersection: 97.6%, and GATK and SAMtools intersection INDELs: 97.6%). We presented two key sources of difficulties in accurate INDEL detection: 1) the presence of repeat, and 2) heterozygous INDELs. Herein we could suggest the accessible algorithms that selectively reduce error rates and thereby facilitate INDEL detection. Our study may also serve as a basis for understanding the accuracy and completeness of INDEL detection. |
| first_indexed | 2024-12-23T11:58:36Z |
| format | Article |
| id | doaj.art-0fe158860ce5418f90bf33f0655918fc |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-23T11:58:36Z |
| publishDate | 2017-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-0fe158860ce5418f90bf33f0655918fc2022-12-21T17:48:01ZengPublic Library of Science (PLoS)PLoS ONE1932-62032017-01-01128e018227210.1371/journal.pone.0182272Optimized detection of insertions/deletions (INDELs) in whole-exome sequencing data.Bo-Young KimJung Hoon ParkHye-Yeong JoSoo Kyung KooMi-Hyun ParkInsertion and deletion (INDEL) mutations, the most common type of structural variance, are associated with several human diseases. The detection of INDELs through next-generation sequencing (NGS) is becoming more common due to the decrease in costs, the increase in efficiency, and sensitivity improvements demonstrated by the various sequencing platforms and analytical tools. However, there are still many errors associated with INDEL variant calling, and distinguishing INDELs from errors in NGS remains challenging. To evaluate INDEL calling from whole-exome sequencing (WES) data, we performed Sanger sequencing for all INDELs called from the several calling algorithm. We compared the performance of the four algorithms (i.e. GATK, SAMtools, Dindel, and Freebayes) for INDEL detection from the same sample. We examined the sensitivity and PPV of GATK (90.2 and 89.5%, respectively), SAMtools (75.3 and 94.4%, respectively), Dindel (90.1 and 88.6%, respectively), and Freebayes (80.1 and 94.4%, respectively). GATK had the highest sensitivity. Furthermore, we identified INDELs with high PPV (4 algorithms intersection: 98.7%, 3 algorithms intersection: 97.6%, and GATK and SAMtools intersection INDELs: 97.6%). We presented two key sources of difficulties in accurate INDEL detection: 1) the presence of repeat, and 2) heterozygous INDELs. Herein we could suggest the accessible algorithms that selectively reduce error rates and thereby facilitate INDEL detection. Our study may also serve as a basis for understanding the accuracy and completeness of INDEL detection.http://europepmc.org/articles/PMC5549930?pdf=render |
| spellingShingle | Bo-Young Kim Jung Hoon Park Hye-Yeong Jo Soo Kyung Koo Mi-Hyun Park Optimized detection of insertions/deletions (INDELs) in whole-exome sequencing data. PLoS ONE |
| title | Optimized detection of insertions/deletions (INDELs) in whole-exome sequencing data. |
| title_full | Optimized detection of insertions/deletions (INDELs) in whole-exome sequencing data. |
| title_fullStr | Optimized detection of insertions/deletions (INDELs) in whole-exome sequencing data. |
| title_full_unstemmed | Optimized detection of insertions/deletions (INDELs) in whole-exome sequencing data. |
| title_short | Optimized detection of insertions/deletions (INDELs) in whole-exome sequencing data. |
| title_sort | optimized detection of insertions deletions indels in whole exome sequencing data |
| url | http://europepmc.org/articles/PMC5549930?pdf=render |
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