Inversion Report: HsInv0072

Human Polymorphic Inversion DataBase

Inversion Report: HsInv0072

General information

Accession	HsInv0072	Region of the inversion	chrX:45432027-45436826
Status	Validated	Prediction type	Simple
Estimated Inversion Size	3,644 bp	Supporting predictions	7
Inverted allele frequency	0.9722	Mechanism of origin	NAHR
Functional effect	Intergenic breakpoints	Breakpoint 1	chrX:45432027-45433183
Ancestral orientation	Inverted	Breakpoint 2	chrX:45435670-45436826

- Region map

+ Predictions

- 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

chrX:45431992-45431992

Breakpoint 2

chrX:45436826-45436826

Individuals

CHM1

- Pang et al. 2010

Description	Paired-end mapping analysis of the J. Craig Venter genome (HuRef)
Method	Paired-end mapping (PEM)

Name

Breakpoint 1

chrX:45432318-45433067

Breakpoint 2

chrX:45435883-45437526

Individuals

HuRef

- 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

chrX:45431978-45433256

Breakpoint 2

chrX:45435577-45437068

Individuals

NA18507

- 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

chrX:45432055-45432055

Breakpoint 2

chrX:45433454-45433454

Individuals

NA15510	NA18505

Name

Breakpoint 1

chrX:45434485-45434485

Breakpoint 2

chrX:45437272-45437272

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

chrX:45433293-45433293

Breakpoint 2

chrX:45435559-45435559

Individuals

HuRef

- Martinez-Fundichely et al. 2014 (in preparation)

Description	Accurate prediction of inversions in the human genome from Kidd et al. 2008 fosmid paired-end mapping data using the GRIAL algorithm, and validation of some predictions by sequence analysis and PCR
Method	Paired-end mapping (PEM)

Name

Breakpoint 1

chrX:45397681-45432601

Breakpoint 2

chrX:45436090-45473696

D/C Score

Disc. Support Prob.

0.98359

Support

7 probes

Individuals

NA12156	NA12878	NA15510	NA18507	NA18517	NA18555	NA18956	NA19129	NA19240

+ Validation and genotyping

-Vicente-Salvador et al. 2017

Description

Validation and characterization of human inversions predicted by comparison of two independently assembled human genomes

Method	Polymerase chain reaction (PCR)
Status	Validated
Genotyping	10 individuals: 8 HapMap/1000GP, 2 Other 1 STD/STD - 7 INV/INV - 2 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.

Method	Inverse polymerase chain reaction (iPCR)
Status	Validated
Genotyping	98 individuals: 96 HapMap/1000GP, 2 Other 1 STD/STD - 1 STD/INV - 50 INV/INV - 46 INV

Status
Force status
Comment

+ Validation details

+ Individuals:

+ Frequency without genotypes:

+ Manually curated breakpoints:

-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	Sequence analysis
Status	Validated
Comment	Inversion validated by analysis of CH17-280N1 BAC sequence (AC255398) obtained with PacBio long reads

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) (Vicente-Salvador et al. 2017)	4	5	0.2857	0.7143	> 0.05

Africa (AFR)	Africa (AFR) summary	4	5	0.2857	0.7143	> 0.05

+ 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) (Vicente-Salvador et al. 2017)	64	93	0.0106	0.9894	> 0.5

Europe (EUR)	Europe (EUR) summary	64	93	0.0106	0.9894	> 0.5

+ 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) (Vicente-Salvador et al. 2017)	1	2	0.0000	1.0000	NA
Japanese	Japanese in Tokyo, Japan (JPT) (Vicente-Salvador et al. 2017)	1	2	0.0000	1.0000	NA

East Asia (EAS)	East Asia (EAS) summary	2	4	0.0000	1.0000	NA

+ 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	0.0000	1.0000	NA

Unknown	Unknown summary	2	3	0.0000	1.0000	NA

+ Breakpoints

Breakpoint 1	chrX:45432027-45433183	Breakpoint 2	chrX:45435670-45436826
Study	Vicente-Salvador et al. 2017
Description	Breakpoints defined by comparison with the updated GRCh38 Human Reference assembly, the HuRef Human Genome assembly and two sequenced fosmids
Definition method	Manual curation
Mechanism of origin	NAHR

Flexibility

10.35

GC content

0.31

Stability

1.79

Comments

Inversion generated by non-allelic homologous recombination (NAHR) between 1.4 kb inverted L1PA13 elements with 98.4% identity

Sequence features

Transposable elements:

Type	Position TE1	Size (bp)	Position TE2	Size (bp)	Identity	Relative orientation
L1PA13	chrX:45431993-45433440	1,448	chrX:45435413-45436856	1,444	98.4	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.

Ancestral allele	Inverted	Age	ND
Derived allele	Standard	Origin	ND

Breakpoint 1	chrX:45432293-45432601	Breakpoint 2	chrX:45436090-45436559
Assembly	hg18
Definition method	Default informatic definition

Breakpoint 1	chrX:45432293-45432601	Breakpoint 2	chrX:45436090-45436559
Assembly	hg18
Definition method	Default informatic definition

Breakpoint 1	chrX:45432293-45432601	Breakpoint 2	chrX:45436090-45436559
Assembly	hg18
Definition method	Default informatic definition

Breakpoint 1	chrX:45432293-45432601	Breakpoint 2	chrX:45436090-45436559
Assembly	hg18
Definition method	Default informatic definition

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