Table 2 Summary of diagnoses and detection methods in the 454 diagnosed probands

Variant type	Analysis method	No. of diagnoses
Chromosomal aneuploidy	Chromosome read-depth counter	2
Copy-number variants	CNsolidate/CoNVex/CIPHER	50
De novo SNVs/indels in known genes	DeNovoGear	232
De novo SNVs/indels in new DDD genes	DeNovoGear/Discovery	58
De novo SNVs/indels in new external genes	DeNovoGear/DDD Research Variant Track	5
De novo indels in known genes	GATK candidate de novo variant	4
Inherited SNVs/indels in known genes	GATK Mendelian filter	82
Inherited SNVs/indels in new DDD genes	GATK Mendelian filter/Discovery	4
Large insertions/deletions	Soft-clipped reads	4
Mosaic structural variants	triPOD	5
Mosaic inherited SNVs/indels	Parental mosaicism	4
Nonessential splice variants	Splicing analysis	4
Uniparental disomy	UPDio	6
Total ^a	All	460

DDD, Deciphering Developmental Disorders study; GATK, Genome Analysis Toolkit; indel, insertion/deletion; SNV, single-nucleotide variant.
Reported variants that were considered by our clinical teams to explain all or part of a patient’s phenotype are summarized here; the variants themselves are available with associated phenotypes through DECIPHER (https://decipher.sanger.ac.uk). All variants are in published developmental disorder genes with sufficient evidence to merit inclusion on our clinician-curated gene-to-phenotype database (https://www.ebi.ac.uk/gene2phenotype/). Note that although most variants have been analytically validated in an accredited diagnostic laboratory, functional studies have not been systematically performed to confirm clinical pathogenicity. Discovery indicates that a new developmental gene was found and published by the DDD study.^12,13,31
^aIncludes six dual diagnoses.

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