Inversion Report: HsInv0045

Human Polymorphic Inversion DataBase

Inversion Report: HsInv0045

General information

Accession	HsInv0045	Region of the inversion	chr21:26942440-26943617
Status	Validated	Prediction type	Simple
Estimated Inversion Size	1,060 bp	Supporting predictions	5
Inverted allele frequency	0.4722	Mechanism of origin	NH
Functional effect	Intergenic breakpoints	Breakpoint 1	chr21:26942440-26942558
Ancestral orientation	Standard	Breakpoint 2	chr21:26943499-26943617

- Region map

+ Predictions

- Hehir-Kwa et al. 2016

Description	Discovery, genotyping and phasing of structural variants detected from Illumina whole genome sequencing data of 769 individuals from 250 Dutch families belonging to the GoNL project
Method	Paired-end mapping (PEM)

Name
Breakpoint 1	chr21:26942221-26942221	Breakpoint 2	chr21:26943371-26943371
Individuals

- 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	chr21:26942524-26942524	Breakpoint 2	chr21:26943582-26943582
Individuals	1977 out of 2504 individuals

- 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

chr21:26940471-26940471

Breakpoint 2

chr21:26942856-26942856

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

chr21:26942554-26942554

Breakpoint 2

chr21:26943508-26943508

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

chr21:26907661-26942554

Breakpoint 2

chr21:26942694-26985712

D/C Score

Disc. Support Prob.

0.99951

Support

2 probes

Individuals

NA12156	NA12878	NA15510	NA18507	NA18517	NA18555	NA18956	NA19129	NA19240

- 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	6	0.2500	0.7500	< 0.05

Africa (AFR)	Africa (AFR) summary	4	6	0.2500	0.7500	< 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	57	0.5547	0.4453	> 0.05

Europe (EUR)	Europe (EUR) summary	64	57	0.5547	0.4453	> 0.05

+ 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	1	0.7500	0.2500	> 0.5

Unknown	Unknown summary	2	1	0.7500	0.2500	> 0.5

+ Breakpoints

Breakpoint 1	chr21:26942440-26942558	Breakpoint 2	chr21:26943499-26943617
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

10.17

GC content

0.61

Stability

2.12

Comments

Inversion generated probably by a non-homologous mechanism (NHEJ or FoSTeS) that could be mediated by inverted AluSx1 elements with ~85.6% identity and it is associated with a 94 bp deletion in BP2

Sequence features

Transposable elements:

Type	Position TE1	Size (bp)	Position TE2	Size (bp)	Identity	Relative orientation
AluSx1	chr21:26942303-26942558	256	chr21:26943499-26943755	257	85.6	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	Standard	Age	ND
Derived allele	Inverted	Origin	ND

Breakpoint 1	chr21:26941554-26942554	Breakpoint 2	chr21:26942694-26944508
Assembly	hg18
Definition method	Default informatic definition

Breakpoint 1	chr21:26941554-26942554	Breakpoint 2	chr21:26942694-26944508
Assembly	hg18
Definition method	Default informatic definition

Breakpoint 1	chr21:26941554-26942554	Breakpoint 2	chr21:26942694-26944508
Assembly	hg18
Definition method	Default informatic definition

Method	Polymerase chain reaction (PCR)
Status	Validated
Genotyping	10 individuals: 8 HapMap/1000GP, 2 Other 4 STD/STD - 1 STD/INV - 5 INV/INV

Method	Inverse polymerase chain reaction (iPCR)
Status	Validated
Genotyping	98 individuals: 96 HapMap/1000GP, 2 Other 28 STD/STD - 55 STD/INV - 15 INV/INV

Method	Sequence analysis
Status	Validated
Comment	Simple inversion validated by sequence analysis of PacBio long reads from fosmids

Species	Orientation	Method	Study
Chimpanzee	Deleted allele	Genome sequence comparison	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