ABraOM

Overview

Illumina Connected Annotation provides allele frequency annotations from ABraOM which is a repository of genomic variants from individual in Sao Paolo, Brazil.

Publication

Naslavsky MS, Santos R, Rudan I, et al. ABraOM: A Brazilian database of genomic variants from whole exome sequenced elderly individuals. Hum Mutat. 2017;38(7):751-763. doi:10.1002/humu.23211

ABraOM has data for both GRCh37 and GRCh38.

Assembly	Name	Description
GRCh37	SABE609	ABraOM dataset for GRCh37, coming from exome samples from 609 individuals
GRCh38	SABE-WGS-1171	ABraOM dataset for GRCh38, coming from whole genome samples from 1171 individuals

Data input

Below are some examples of entry for SABE609 dataset.

Chr Start   Ref Alt PredictedFunc.refGene   Gene.refGene    PredConsequence.refGene avsnp147    FILTER  CEGH Filter HomozygousALT count Hemizygous count    Allele number   Allele ALT count    Frequencies Cohort
1   13116   T   G   ncRNA_intronic  DDX11L1 NA  rs62635286  LowQual FDP 2   0   598 6   0.010033    SABE609
1   13244   G   A   ncRNA_exonic    DDX11L1 NA  NA  LowQual FAB 0   0   456 1   0.002193    SABE609
1   13248   C   G   ncRNA_exonic    DDX11L1 NA  NA  VQSRTrancheSNP99.00to99.90  FAB 0   0   482 2   0.004149    SABE609
1   13273   G   C   ncRNA_exonic    DDX11L1 NA  rs531730856 VQSRTrancheSNP99.00to99.90  WK-LowCall  20  0   600 68  0.113333    SABE609
1   13302   C   T   ncRNA_exonic    DDX11L1 NA  rs180734498 VQSRTrancheSNP99.00to99.90  WK-LowCall  1   0   700 12  0.017143    SABE609
1   13380   C   G   ncRNA_exonic    DDX11L1 NA  rs571093408 VQSRTrancheSNP99.00to99.90  FAB 0   0   514 4   0.007782    SABE609
...

As for SABE-WGS-1171.

Chr Start   Ref Alt PredictedFunc.refGene   Gene.refGene    PredConsequence.refGene avsnp150    FILTER  CEGH_Filter HomozygousALT_count Hemizygous_count    Allele_number   Allele_ALT_count    Frequencies Cohort
1   10354   C   A   intergenic  DDX11L1;NONE    dist=NONE;dist=1520 rs1015856060    VQSRTrancheSNP99.80to99.90  FDP 6   0   624 12  0.019231    SABE-WGS-1171
1   10378   CCCTAACCCTAACCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC-intergenic  DDX11L1;NONE    dist=NONE;dist=1434     PASS    FDP 20  1080    6   0.005556    SABE-WGS-1171
1   10379   CCTAA   -   intergenic  DDX11L1;NONE    dist=NONE;dist=1491     VQSRTrancheINDEL99.00to99.30    FDP 1   0   1190    20.001681   SABE-WGS-1171
1   10384   CCCTAACCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC   -intergenic DDX11L1;NONE    dist=NONE;dist=1434     PASS    vSR-LowCall 0   0   1042    1   0.000960    SABE-WGS-1171
1   10390   CCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC -   intergenic  DDX11L1;NONE    dist=NONE;dist=1434     PASS    vSR-LowCall 0   0   838 1   0.001193    SABE-WGS-1171
1   10390   C   -   intergenic  DDX11L1;NONE    dist=NONE;dist=1484 rs766767872 PASS    FDP 1   0   842 4   0.004751SABE-WGS-1171
1   10391   CCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA -   intergenic  DDX11L1;NONE    dist=NONE;dist=1441     PASS    WK-LowCall  30  0   902 90  0.099778    SABE-WGS-1171
1   10396   AC  -   intergenic  DDX11L1;NONE    dist=NONE;dist=1477     PASS    FDP 0   0   812 1   0.001232    SABE-WGS-1171
1   10398   CCCTAA  -   intergenic  DDX11L1;NONE    dist=NONE;dist=1471     PASS    FDP 9   0   1004    21  0.020916    SABE-WGS-1171

Parsing

From the TSV file, the following columns are parsed out and provided in the annotation output:

Column	Description	Illumina Connected Annotatyion JSON key
HomozygousALT_count	Homozygous alt allele count number	homozygote
Hemizygous_count	Hemizygous allele count number	hemizygote
Allele_number	Total allele number	allAn
Allele_ALT_count	Number of alt allele	allAc
Frequencies	Frequency of alt allele	allAf

Output

ABraOM supplementary data will have abraom key in Illumina Connected Annotation JSON output. Below is an example of annotation output from ABraOM.

"abraom": {
        "homozygote": 532,
        "hemizygote": 0,
        "allAn": 1164,
        "allAc": 1113,
        "allAf": 0.956186
      }