| Accession | HsInv1116 | Region of the inversion | chr1:185731452-185733355 |
| Status | Validated | Prediction type | Complex |
| Estimated Inversion Size | 1,077 bp | Supporting predictions | 6 |
| Inverted allele frequency | 0.7778 | Mechanism of origin | FoSTeS |
| Functional effect | Intergenic breakpoints | Breakpoint 1 | chr1:185731452-185733101 |
| Ancestral orientation | Standard | Breakpoint 2 | chr1:185733351-185733355 |
| Comments | Derived allele includes two deletions of 1.6 kb and 2 bp flanking the inverted region (which make that some of the predictions are not completely consistent)
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Human Polymorphic Inversion DataBase
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General information
- Region map
+ Predictions
| Description | Identification and resolution of sequence gaps and structural variants in the euchromatic regions of the reference human assembly through single-molecule, real-time (SMRT) DNA sequencing of an haploid human genome (CHM1) | ||||||||||||||
| Method | Long-read sequencing | ||||||||||||||
| Name | |||||||
| Breakpoint 1 | chr1:185733098-185733098 | Breakpoint 2 | chr1:185733350-185733350 | ||||
| Individuals |
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| Description | Next generation sequencing and analysis by paired-end mapping of an individual genome of African origin | ||||||||||||||
| Method | Paired-end mapping (PEM) | ||||||||||||||
| Name | |||||||
| Breakpoint 1 | chr1:185731535-185733095 | Breakpoint 2 | chr1:185733337-185733999 | ||||
| Individuals |
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| Description | Next generation sequencing and analysis by paired-end mapping of a Korean individual genome | ||||||||||||||||||||||||||||||
| Method | Paired-end mapping (PEM) | ||||||||||||||||||||||||||||||
| Name | |||||||
| Breakpoint 1 | chr1:185731223-185731452 | Breakpoint 2 | chr1:185733109-185733352 | ||||
| Individuals |
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| Name | |||||||
| Breakpoint 1 | chr1:185733098-185733238 | Breakpoint 2 | chr1:185733350-185733577 | ||||
| Individuals |
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| Description | Next-generation sequencing and analysis by paired-end mapping of a male Han Chinese individual genome | ||||||||||
| Method | Paired-end mapping (PEM) | ||||||||||
| Name | |||
| Breakpoint 1 | chr1:185731237-185731237 | Breakpoint 2 | chr1:185733252-185733252 |
| Individuals | |||
| Description | Sequencing and analysis of the independently assembled diploid J. Craig Venter genome (HuRef) | ||||||||||||||
| Method | Genome sequence comparison | ||||||||||||||
| Name | |||||||
| Breakpoint 1 | chr1:185733101-185733101 | Breakpoint 2 | chr1:185733350-185733350 | ||||
| Individuals |
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+ Validation and genotyping
| Description | Validation and characterization of human inversions predicted by comparison of two independently assembled human genomes | ||||
| Method | Polymerase chain reaction (PCR) |
| Status | Validated |
| Genotyping | 98 individuals: 96 HapMap/1000GP, 2 Other 6 STD/STD - 33 STD/INV - 59 INV/INV  |
| Description | Identification and resolution of sequence gaps and structural variants in the euchromatic regions of the reference human assembly through single-molecule, real-time (SMRT) DNA sequencing of an haploid human genome (CHM1) | ||||
| Method | Sequence analysis |
| Status | Validated |
| Comment | Inversion validated by analysis of CH17-19N16 BAC sequence (AC255464) obtained with the Illumina Nextera system |
- Frequency
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+ Africa (AFR)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
Yoruba
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Yoruba in Ibadan, Nigeria (YRI) (Vicente-Salvador et al. 2017) | 4 | 7 | 0.1250 | 0.8750 | > 0.5 |
| Africa (AFR)
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Africa (AFR) summary | 4 | 7 | 0.1250 | 0.8750 | > 0.5 |
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+ Europe (EUR)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Northwestern European
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Utah residents with Northern and Western European ancestry (CEU) (Vicente-Salvador et al. 2017) | 64 | 98 | 0.2344 | 0.7656 | > 0.3 |
| Europe (EUR)
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Europe (EUR) summary | 64 | 98 | 0.2344 | 0.7656 | > 0.3 |
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+ East Asia (EAS)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Han Chinese
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Han Chinese in Beijing, China (CHB) (Vicente-Salvador et al. 2017) | 1 | 2 | 0.0000 | 1.0000 | NA |
| Japanese
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Japanese in Tokyo, Japan (JPT) (Vicente-Salvador et al. 2017) | 1 | 2 | 0.0000 | 1.0000 | NA |
| East Asia (EAS)
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East Asia (EAS) summary | 2 | 4 | 0.0000 | 1.0000 | NA |
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+ Unknown
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Unknown
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Unknown (Vicente-Salvador et al. 2017) | 2 | 3 | 0.2500 | 0.7500 | > 0.5 |
| Unknown
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Unknown summary | 2 | 3 | 0.2500 | 0.7500 | > 0.5 |
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+ Breakpoints
| Breakpoint 1 | chr1:185731452-185733101 | Breakpoint 2 | chr1:185733351-185733355 | ||
| Study | Vicente-Salvador et al. 2017 | ||||
| Description | Breakpoints defined by comparison with HuRef Human Genome assembly | ||||
| Definition method | Manual curation | ||||
| Mechanism of origin |
FoSTeS
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| Flexibility | 11.2 | GC content | 0.35 | Stability | 1.78 |
| Comments |
Inverted region is flanked by two deletions of 1.6 kb and 2 bp, and was probably generated by two fork stalling and template switching (FoSTeS) events, at least one of which was mediated by microhomology. Breakpoint positions comprise each deleted sequence. |
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+ Evolutionary history
| Ancestral allele | Standard | Age | ND |
| Derived allele | Inverted | Origin | ND |
+ Orientation in other species
| Species | Orientation | Method | Study |
| Chimpanzee | Standard | Polymerase chain reaction (PCR) | Vicente-Salvador et al. 2017 |
| Gorilla | Standard | Polymerase chain reaction (PCR) | Vicente-Salvador et al. 2017 |
| Rhesus macaque | Standard | Genome sequence comparison | Vicente-Salvador et al. 2017 |
+ Age
Not defined
+ Origin
Not defined
+ Functional effects
No genes disrupted by the inversion breakpoints
+ Inversion phenotypical effects
Not defined
+ Report history
HsInv0631 and HsInv0624 and HsInv0003 merge into HsInv1116
- 2017-09-29 00:00:00
| Breakpoint 1 | chr1:185728098-185738098 | Breakpoint 2 | chr1:185728350-185738350 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2016-12-09 18:59:43
| Breakpoint 1 | chr1:185730852-185734101 | Breakpoint 2 | chr1:185732350-185734350 |
| Assembly | hg18 | ||
| Description | Breakpoints not refined due to lack of overlap of predictions in at least one breakpoint | ||
| Definition method | Default informatic definition | ||
- 2016-12-09 18:59:43
| Breakpoint 1 | chr1:185731452-185733101 | Breakpoint 2 | chr1:185733351-185733355 |
| Study | Vicente-Salvador et al. 2017 | ||
| Assembly | hg18 | ||
| Description | Breakpoints defined by comparison with HuRef Human Genome assembly | ||
| Definition method | Manual curation | ||
Hosted by the Comparative and Functional Genomics group at the Hospital del Mar Research Institute
Contact us at invfestdb@researchmar.net
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