Inversion Report: HsInv1049

Human Polymorphic Inversion DataBase

Inversion Report: HsInv1049

General information

Accession	HsInv1049	Region of the inversion	chr15:28157404-30687000
Status	Validated	Prediction type	Simple
Estimated Inversion Size	2,032,350 bp	Supporting predictions	1
Inverted allele frequency	0.2037	Mechanism of origin	NAHR
Functional effect	Intergenic breakpoints	Breakpoint 1	chr15:28157404-28697597
Ancestral orientation	Standard	Breakpoint 2	chr15:30232700-30687000
Comments	Complex region including five structural configurations as a result of human-specific expansions of segmental duplications and two independent inversion events related to palindromic GOLGA8 core duplicons

- Region map

+ Predictions

+ Validation and genotyping

-Antonacci et al. 2009

Description

Characterization of six large inversion polymorphisms with complex segmental duplications at the breakpoints in 27 individuals from three HapMap populations by a metaphase FISH-based assay

Method	Fluorescence in situ hybridization (FISH)
Status	Validated
Genotyping	27 individuals: 27 HapMap/1000GP 17 STD/STD - 9 STD/INV - 1 INV/INV

Status
Force status
Comment

+ Validation details

+ Individuals:

+ Frequency without genotypes:

Please be aware that this information will be displayed in the Frequency section of the Inversion report, but the following will not be available: Hardy-Weinberg test and genotype file for download. Also, data will not be averaged with other studies of the same population.

Population
Analyzed individuals
Inverted alleles
Standard frequency
Inverted frequency

+ Manually curated breakpoints:

Only modified sections are submitted. All the corresponding fields must be complete because they will be overwritten. In the Frequency without genotypes section multiple populations can be added if the editing process is repeated for each one of them.

-INVFEST curation

Description

Information update by manual analysis of InvFEST curators

Method	Sequence analysis
Status	Breakpoint refinement

Status
Force status
Comment

+ Validation details

+ Individuals:

+ Frequency without genotypes:

+ Manually curated breakpoints:

- Frequency

+ Africa (AFR)

Population	Sample and Study	Independent individuals	Inverted alleles	Standard frequency	Inverted frequency	HWE p-value
Yoruba	Yoruba in Ibadan, Nigeria (YRI) (Antonacci et al. 2009)	11	5	0.7727	0.2273	> 0.3

Africa (AFR)	Africa (AFR) summary	11	5	0.7727	0.2273	> 0.3

+ Europe (EUR)

Population	Sample and Study	Independent individuals	Inverted alleles	Standard frequency	Inverted frequency	HWE p-value
Northwestern European	Utah residents with Northern and Western European ancestry (CEU) (Antonacci et al. 2009)	8	4	0.7500	0.2500	> 0.3

Europe (EUR)	Europe (EUR) summary	8	4	0.7500	0.2500	> 0.3

+ East Asia (EAS)

Population	Sample and Study	Independent individuals	Inverted alleles	Standard frequency	Inverted frequency	HWE p-value
Han Chinese	Han Chinese in Beijing, China (CHB) (Antonacci et al. 2009)	4	1	0.8750	0.1250	> 0.5
Japanese	Japanese in Tokyo, Japan (JPT) (Antonacci et al. 2009)	4	1	0.8750	0.1250	> 0.5

East Asia (EAS)	East Asia (EAS) summary	8	2	0.8750	0.1250	> 0.5

+ Breakpoints

Breakpoint 1	chr15:28157404-28697597	Breakpoint 2	chr15:30232700-30687000
Study	INVFEST curation
Description	Breakpoints defined by InvFEST curators as the largest blocks of inverted segmental duplications
Definition method	Manual curation
Mechanism of origin	NAHR

Flexibility

10.79

GC content

0.49

Stability

1.96

Comments

Inversion generated by non-allelic homologous recombination (NAHR) between large blocks of inverted SDs with high identity

Sequence features

Segmental duplications:

Position SD1	Size (bp)	Position SD2	Size (bp)	Identity	Relative orientation
chr15:28157403-28457303	299,901	chr15:30232699-30540153	307,455	0.996	Inverted
chr15:28157403-28176535	19,133	chr15:30667922-30687000	19,079	0.980	Direct
chr15:28212797-28228597	15,801	chr15:30671215-30687000	15,786	0.982	Direct
chr15:28479703-28697597	217,895	chr15:30468739-30687000	218,262	0.996	Inverted

+ Evolutionary history

+ Functional effects

+ Report history

Hosted by the Comparative and Functional Genomics group at the Universitat Autònoma de Barcelona

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Ancestral allele	Standard	Age	ND
Derived allele	Inverted	Origin	ND

Name
Breakpoint 1	chr15:28157404-28697597	Breakpoint 2	chr15:30232700-30687000
Individuals
Comments	Breakpoints defined by INVFEST to include all pairs of inverted segmental duplications located at both predicted breakpoint regions

Species	Orientation	Method	Study
Chimpanzee	Standard	Fluorescence in situ hybridization (FISH)	Antonacci et al. 2009
Bonobo	Standard	Fluorescence in situ hybridization (FISH)	Antonacci et al. 2009
Gorilla	Standard	Fluorescence in situ hybridization (FISH)	Antonacci et al. 2009
Orangutan	Standard	Fluorescence in situ hybridization (FISH)	Antonacci et al. 2009