TY - JOUR
T1 - Reference exome data for a Northern Brazilian population
AU - Weeks, Alexia L.
AU - Francis, Richard W.
AU - Neri, Joao I.C.F.
AU - Costa, Nathaly M.C.
AU - Arrais, Nivea M.R.
AU - Lassmann, Timo
AU - Blackwell, Jenefer M.
AU - Jeronimo, Selma M.B.
PY - 2020/12/1
Y1 - 2020/12/1
N2 - Exome sequencing is widely used in the diagnosis of rare genetic diseases and provides useful variant data for analysis of complex diseases. There is not always adequate population-specific reference data to assist in assigning a diagnostic variant to a specific clinical condition. Here we provide a catalogue of variants called after sequencing the exomes of 45 babies from Rio Grande do Nord in Brazil. Sequence data were processed using an ‘intersect-then-combine’ (ITC) approach, using GATK and SAMtools to call variants. A total of 612,761 variants were identified in at least one individual in this Brazilian Cohort, including 559,448 single nucleotide variants (SNVs) and 53,313 insertion/deletions. Of these, 58,111 overlapped with nonsynonymous (nsSNVs) or splice site (ssSNVs) SNVs in dbNSFP. As an aid to clinical diagnosis of rare diseases, we used the American College of Medicine Genetics and Genomics (ACMG) guidelines to assign pathogenic/likely pathogenic status to 185 (0.32%) of the 58,111 nsSNVs and ssSNVs. Our data set provides a useful reference point for diagnosis of rare diseases in Brazil. (169 words).
AB - Exome sequencing is widely used in the diagnosis of rare genetic diseases and provides useful variant data for analysis of complex diseases. There is not always adequate population-specific reference data to assist in assigning a diagnostic variant to a specific clinical condition. Here we provide a catalogue of variants called after sequencing the exomes of 45 babies from Rio Grande do Nord in Brazil. Sequence data were processed using an ‘intersect-then-combine’ (ITC) approach, using GATK and SAMtools to call variants. A total of 612,761 variants were identified in at least one individual in this Brazilian Cohort, including 559,448 single nucleotide variants (SNVs) and 53,313 insertion/deletions. Of these, 58,111 overlapped with nonsynonymous (nsSNVs) or splice site (ssSNVs) SNVs in dbNSFP. As an aid to clinical diagnosis of rare diseases, we used the American College of Medicine Genetics and Genomics (ACMG) guidelines to assign pathogenic/likely pathogenic status to 185 (0.32%) of the 58,111 nsSNVs and ssSNVs. Our data set provides a useful reference point for diagnosis of rare diseases in Brazil. (169 words).
UR - http://www.scopus.com/inward/record.url?scp=85093855160&partnerID=8YFLogxK
U2 - 10.1038/s41597-020-00703-y
DO - 10.1038/s41597-020-00703-y
M3 - Data article
C2 - 33087711
AN - SCOPUS:85093855160
SN - 2052-4463
VL - 7
JO - Scientific Data
JF - Scientific Data
IS - 1
M1 - 360
ER -