Revista salvadoreña sobre temas relacionados al café, sus aspectos económicos, técnicos,cultivo,historia,Asociaciones e información variada.Esta es una publicación de la Junta Departamental de la "Asociación Cafetalera de El Salvador" y Portavoz de la Junta Departamental de la "Asociación de Ganaderos de El Salvador".— Todos los meses del año de 1946 guardados en un solo archivo. – Contenido : Enero, No. 136 (págs. 1-38) – Febrero, No. 137 (págs. 39-70) – Marzo, No. 138 (págs. 71-102) – Abril, No. (págs. 103-134) – Mayo, No. (págs. 135-166) – Junio No. (págs. 167-198) – Julio, No. 142 (págs. 199-230) – Agosto, No. 143 (págs. 231-262) – Septiembre, No. 144 (págs. 263-294) – Octubre, No. 145 (págs. 295-326) – Noviembre, No. 147 (págs. 359-388

Alexandra Buckley (4104160)

Hannah Carter (276508)

Kristopher Standish (3450338)

Kunal Bhutani (4104157)

Nicholas Schork (332955)

Olivier Harismendy (239761)

Roger Lasken (220114)

Trey Ideker (10055)

BMC Genomics

Technical covariates for 9618 samples in pan-cancer cohort. (XLSX 600Â kb

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Additional file 2: of Pan-cancer analysis reveals technical artifacts in TCGA germline variant calls

BackgroundCancer research to date has largely focused on somatically acquired genetic aberrations. In contrast, the degree to which germline, or inherited, variation contributes to tumorigenesis remains unclear, possibly due to a lack of accessible germline variant data. Here we called germline variants on 9618 cases from The Cancer Genome Atlas (TCGA) database representing 31 cancer types.ResultsWe identified batch effects affecting loss of function (LOF) variant calls that can be traced back to differences in the way the sequence data were generated both within and across cancer types. Overall, LOF indel calls were more sensitive to technical artifacts than LOF Single Nucleotide Variant (SNV) calls. In particular, whole genome amplification of DNA prior to sequencing led to an artificially increased burden of LOF indel calls, which confounded association analyses relating germline variants to tumor type despite stringent indel filtering strategies. The samples affected by these technical artifacts include all acute myeloid leukemia and practically all ovarian cancer samples.ConclusionsWe demonstrate how technical artifacts induced by whole genome amplification of DNA can lead to false positive germline-tumor type associations and suggest TCGA whole genome amplified samples be used with caution. This study draws attention to the need to be sensitive to problems associated with a lack of uniformity in data generation in TCGA data

Buckley, Alexandra R

Standish, Kristopher A

Bhutani, Kunal

Ideker, Trey

Lasken, Roger S

Carter, Hannah

Harismendy, Olivier

Schork, Nicholas J

eScholarship - University of California

Pan-cancer analysis reveals technical artifacts in TCGA germline variant calls

Asociación Cafetalera de El Salvador

Repositorio Digital de la Ciencia y Cultura de El Salvador REDICCES

Spanish

Lamatepec, ene.-dic. 1946, Epoca II, año X, XII, No. 136-147

Abstract Background Cancer research to date has largely focused on somatically acquired genetic aberrations. In contrast, the degree to which germline, or inherited, variation contributes to tumorigenesis remains unclear, possibly due to a lack of accessible germline variant data. Here we called germline variants on 9618 cases from The Cancer Genome Atlas (TCGA) database representing 31 cancer types. Results We identified batch effects affecting loss of function (LOF) variant calls that can be traced back to differences in the way the sequence data were generated both within and across cancer types. Overall, LOF indel calls were more sensitive to technical artifacts than LOF Single Nucleotide Variant (SNV) calls. In particular, whole genome amplification of DNA prior to sequencing led to an artificially increased burden of LOF indel calls, which confounded association analyses relating germline variants to tumor type despite stringent indel filtering strategies. The samples affected by these technical artifacts include all acute myeloid leukemia and practically all ovarian cancer samples. Conclusions We demonstrate how technical artifacts induced by whole genome amplification of DNA can lead to false positive germline-tumor type associations and suggest TCGA whole genome amplified samples be used with caution. This study draws attention to the need to be sensitive to problems associated with a lack of uniformity in data generation in TCGA data

Lamatepec, ene.-dic. 1946, Epoca II, año X, XII, No. 136-147

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Repositorio Digital de la Ciencia y Cultura de El Salvador REDICCES

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