Comprehensive Genetic Profiling Pipeline

A protocol24 (link) using the Agilent (Santa Clara, California, USA) ClearSeq Inherited Disease panel kit for enrichment followed by NGS targeted on 2742 genes was adapted for the clinical testing of every enrolled proband. For variant calling, GATK best practice was employed for SNV/small indels. CANOES25 (link) and HMZDelFinder12 (link) were separately applied for CNV detection, and the results were merged. The annotation and filtrations of both SNVs and CNVs followed those reported in published works.26 27 Detailed descriptions of the sequencing, variant calling, annotation and filtering processes can be found in the online supplementary notes and online supplementary figure S1.

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Dong X., Liu B., Yang L., Wang H., Wu B., Liu R., Chen H., Chen X., Yu S., Chen B., Wang S., Xu X., Zhou W, & Lu Y. (2020). Clinical exome sequencing as the first-tier test for diagnosing developmental disorders covering both CNV and SNV: a Chinese cohort. Journal of Medical Genetics, 57(8), 558-566.

Publication 2020

ClearSeq Inherited Disease panel kit

Filtrations Genes Indels Inherited disease

Corresponding Organization : Children's Hospital of Fudan University

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Protocol cited in 9 other protocols

Variable analysis

independent variables

Agilent (Santa Clara, California, USA) ClearSeq Inherited Disease panel kit for enrichment
GATK best practice for SNV/small indels variant calling
CANOES and HMZDelFinder for CNV detection
Annotation and filtrations of both SNVs and CNVs

dependent variables

Variant calling results
CNV detection results

control variables

Not explicitly mentioned

controls

No positive or negative controls were explicitly mentioned in the provided text.

Annotations

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