The Team

Faculty: Prof. Mayana Zatz, PhD and Prof. Maria Rita Passos-Bueno, PhD

Cohort provided by: Prof. Maria Lucia Lebrão, MD/PhD (in memoriam) and Prof. Yeda A. O Duarte, PhD

ABraOM project leaders: Michel S. Naslavsky, PhD and Guilherme Lopes Yamamoto, MD

Technical and scientific support: Suzana Ezquina, PhD, Nam Pho, MSc, Daniel Bozoklian, BSc, Daniele Yumi, PhD and Tatiana Orli Milkewitz Sandberg, BSc


Citation

"Exomic variants of an elderly cohort of Brazilians in the ABraOM database"

by Naslavsky, Yamamoto et al. is published in Human Mutation:

http://onlinelibrary.wiley.com/doi/10.1002/humu.23220/full

SABE609 Cohort

Longitudinal study (every five years) with cross-sectional features. In every time-point a new cohort is added in with the same sampling methodology.
Boxes in black represent number of individuals enrolled in each collection. In red, individuals collected in year 2010: performed WES/total.
Variants from all 609 that were sequenced are disposed in ABraOM.

CEGH-USP Flagging

Flagging algorythm with criteria based on depth of coverage (≥10 reads) and allele balance [between 0.3 and 0.7 (heterozygous), below 0.1 (reference homozygous) and above 0.9 (alternate homozygous) proportion of reference allele over sum of reference and alternate]. Two cutoffs were used: proportion of alternate genotypes that don’t fit criteria among all alternate genotypes and total number of genotypes that fit criteria. 100% proportion: FDP (>50% of called genotypes haven’t met minimum depth) or FAB (≤ 50% were flagged as low DP, therefore most genotypes were off allele balance thresholds); ≥50%: WK (≥250 genotypes) or WK-LowCall (<250 genotypes); from 10-50%: SR (≥250 genotypes) or SR-LowCall (<250 genotypes); ≤ 10% vSR (≥250 genotypes) or vSR-LowCall (<250 genotypes). Variants with vSR, SR, WK, vSR-LowCall, SR-LowCall and WK-LowCall flags are probably true, with varying levels of confidence. Variants with FDP or FAB are probably false (although called, no variants met criteria). FAB is checked only after FDP was applied. Multiallelic variants were split, but genotypes other than 0/0, 0/1 and 1/1 were not included in this preliminary analysis.







Summary statistics

1. General
# SAMPLES : 609
# VARIANTS : 2382573

2. Genotypes

2.1 Biallelic
# 0/0 : 1065666852
# 0/1 : 61374709
# 1/1 : 46563363

2.2 Multiallelic or uncalled
# 1/. : 1403915
# ./1 : 1403915
# 0/. : 11142906
# ./0 : 0
# ./. : 8274338
# else : 0

3. Depth (all, including off targets)
3.1 Total Depth of the file: 50805310209 bases.
3.2 Mean Depth per Genotype: 35.01 reads/genotype



Human Genome and Stem Cell
Research Center - HUG-CELL

The University of Sao Paulo
Rua do Matão - Travessa 13, n. 106
Cidade Universitária, São Paulo, SP
CEP: 05508-090
HUG-CELL Website


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Contact


abraom@ib.usp.br