Inversion Report: HsInv0031

Human Polymorphic Inversion DataBase

Inversion Report: HsInv0031

General information

Accession	HsInv0031	Region of the inversion	chr16:83746215-83747305
Status	Validated	Prediction type	Simple
Estimated Inversion Size	1,065 bp	Supporting predictions	7
Inverted allele frequency	0.6761	Mechanism of origin	NH
Functional effect	Intergenic breakpoints	Breakpoint 1	chr16:83746215-83746259
Ancestral orientation	Inverted	Breakpoint 2	chr16:83747296-83747305

- Region map

+ Predictions

- Sudmant et al. 2015

Description	Integrated analysis of structural variants in 2,504 human genomes through short-read and long-read DNA sequencing and statistical imputation using the 1000 Genomes Project data
Method	Paired-end mapping (PEM), Long-read sequencing

Name
Breakpoint 1	chr16:83746140-83746140	Breakpoint 2	chr16:83747324-83747324
Individuals	2092 out of 2504 individuals

- Chaisson et al. 2015

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

chr16:83746214-83746214

Breakpoint 2

chr16:83747303-83747303

Individuals

CHM1

- McKernan et al. 2009

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

chr16:83746155-83746300

Breakpoint 2

chr16:83747137-83747328

Individuals

NA18507

- Ahn et al. 2009

Description	Next generation sequencing and analysis by paired-end mapping of a Korean individual genome
Method	Paired-end mapping (PEM)

Name

Breakpoint 1

chr16:83746234-83746333

Breakpoint 2

chr16:83747453-83747513

Individuals

SJK

- Korbel et al. 2007

Description	Paired-end mapping of 3-kb fragments in an African and in a putatively European individual with some predictions validated by PCR, fiber-FISH or comparison with Celera assembly
Method	Paired-end mapping (PEM)

Name

Breakpoint 1

chr16:83746823-83746823

Breakpoint 2

chr16:83748870-83748870

Individuals

NA15510	NA18505

- Levy et al. 2007

Description	Sequencing and analysis of the independently assembled diploid J. Craig Venter genome (HuRef)
Method	Genome sequence comparison

Name

Breakpoint 1

chr16:83746237-83746237

Breakpoint 2

chr16:83747302-83747302

Individuals

HuRef

- Feuk et al. 2005

Description	Identification of human inversion polymorphisms by comparative analysis of human and chimpanzee genome sequence assemblies
Method	Genome sequence comparison

Name
Breakpoint 1	chr16:83746237-83746238	Breakpoint 2	chr16:83747302-83747303
Individuals

- Frequency

+ Africa (AFR)

Population	Sample and Study	Independent individuals	Inverted alleles	Standard frequency	Inverted frequency	HWE p-value
Yoruba	All samples and studies	4	6	0.2500	0.7500	> 0.5

Africa (AFR)	Africa (AFR) summary	4	6	0.2500	0.7500	> 0.5

+ Europe (EUR)

Population	Sample and Study	Independent individuals	Inverted alleles	Standard frequency	Inverted frequency	HWE p-value
Northwestern European	All samples and studies	63	85	0.3254	0.6746	> 0.3

Europe (EUR)	Europe (EUR) summary	63	85	0.3254	0.6746	> 0.3

+ East Asia (EAS)

Population	Sample and Study	Independent individuals	Inverted alleles	Standard frequency	Inverted frequency	HWE p-value
Han Chinese	All samples and studies	1	1	0.5000	0.5000	> 0.3
Japanese	All samples and studies	1	1	0.5000	0.5000	> 0.3

East Asia (EAS)	East Asia (EAS) summary	2	2	0.5000	0.5000	> 0.1

+ Unknown

Population	Sample and Study	Independent individuals	Inverted alleles	Standard frequency	Inverted frequency	HWE p-value
Unknown	Unknown (Vicente-Salvador et al. 2017)	2	3	0.2500	0.7500	> 0.5

Unknown	Unknown summary	2	3	0.2500	0.7500	> 0.5

+ Breakpoints

Breakpoint 1	chr16:83746215-83746259	Breakpoint 2	chr16:83747296-83747305
Study	Vicente-Salvador et al. 2017
Description	Breakpoints defined by comparison with HuRef Human Genome assembly
Definition method	Manual curation
Mechanism of origin	NH

Flexibility

9.98

GC content

0.59

Stability

2.04

Comments

Inversion generated probably by a non-homologous mechanism (NHEJ or FoSTeS) that could be mediated by inverted AluSq2 and AluSx1 elements with ~83.2% identity and it is associated with a 35 bp deletion in BP2

Sequence features

Transposable elements:

Type	Position TE1	Size (bp)	Position TE2	Size (bp)	Identity	Relative orientation
AluSq2/AluSx1	chr16:83746171-83746455	285	chr16:83747100-83747348	249	83.2	Inverted

+ Evolutionary history

+ Functional effects

+ Report history

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

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Method	Genotype predicted by tag-SNPs
Status	Genotyping
Genotyping	206 individuals (No genotypes available)
Comment	Inversion genotypes estimated from association with tag SNP rs9933231 (r2 > 0.8)

Ancestral allele	Inverted	Age	ND
Derived allele	Standard	Origin	ND

Breakpoint 1	chr16:83745733-83746834	Breakpoint 2	chr16:83746913-83748053
Assembly	hg18
Definition method	Default informatic definition

Method	Polymerase chain reaction (PCR)
Status	Validated
Genotyping	10 individuals: 8 HapMap/1000GP, 2 Other 5 STD/INV - 5 INV/INV

Method	Inverse polymerase chain reaction (iPCR)
Status	Validated
Genotyping	98 individuals: 96 HapMap/1000GP, 2 Other 8 STD/STD - 48 STD/INV - 41 INV/INV - 1 ND
Comment	Inversion validated in 10 individuals of diverse origin by regular PCR and genotyped in 90 CEU individuals by inverse PCR

Method	Sequence analysis
Status	Validated
Comment	Inversion validated by analysis of CH17-3D1 BAC sequence (AC255458) obtained with the Illumina Nextera system

Species	Orientation	Method	Study
Chimpanzee	Inverted	Polymerase chain reaction (PCR)	Vicente-Salvador et al. 2017
Gorilla	Inverted	Polymerase chain reaction (PCR)	Vicente-Salvador et al. 2017