Template for Exome Report
1.
Abstract. The abstract should include the list of all the genes that are discussed in the variation section
2.
Clinical description. Provide full case report.

Mention sex, ethnicity, parental age, biometry at birth (and gestational age), biometry at last
investigation - both with centiles and/or standard deviations, psychomotor development (if
possible include IQ or DQ, with the test used and at what age), phenotype at last examination,

current age, and all pertinent elements of clinical history.
Use the Standard Terminology proposed in Elements of Morphology or Human Phenotype
Ontology (vide supra). Give pertinent family information.
3.
Methods : please include




Capture method
Type of sequencer
Variant analysis strategies (home-made pipeline, public tools…)
List of databases checked (Exome Variant Server, 1000 Genomes,…) and date on which the check was
done.
4.
NGS quality report summary for each sample
Template of the quality report table (download xls file) to be inserted in the manuscript.
Proband
Total captured regions size
% of captured regions with coverage >10
Average coverage of captured region (%)
Total number of SNPs
Total number of INDELs
5.
Add other family
members (parents,
sibs…) as appropriate
Mb
%
%
Variations of interest
5.1. Variations reported online
All variants that fulfill one of the technical and biological criteria below must be declared in DECIPHER prior to final
acceptance. The ID number of the DECIPHER data must be declared here. Declaration to other databases may
be added here as well.
A. Technical requirements
1.
For single nucleotide variations: coverage ≥10 in proband and relatives, with raw alignment checked in
2.
parents
For indels: >5 variant reads and a variant/reference read ratio >0.3
B. Genetic conditions
1.
2.
3.
heterozygous variants/indel present in the proband and absent in unaffected parents and controls;
homozygous variants/indel and hemizygous X variants never reported in public databases
genes with two rare non synonymous variants/indel with mean allelic frequency <0.03, present in the
proband, but not seen together in the parents and controls
The declaration is made using this DECIPHER xls file provided. All items, including those that are not mandatory
for DECIPHER, must be completed, according to DECIPHER keywords. The main phenotypic traits must be
added using HPO.
5.2. Subset of variations reported in the manuscript
Among variants, all variants that

have predicted pathogenicity (definite or probable) by at least one prediction program and

occur in genes that could be hypothesized to be associated with the phenotype based on current
knowledge of gene function, pathway, expression pattern and suspected inheritance mode must be
presented in a tabular form (see an example below with three type of variations) and discussed. All these
variants must have been checked by Sanger sequencing in the proband and the relevant relatives, and
must be further discussed in the text of this section.
Secondary/incidental findings in genes unrelated to the phenotype will not been reported.
Template for variants of interest (download xls file) to be inserted in the manuscript
Chromosome
chr1
chr7
chr12
Position
239040006
45214519
45214604
Gene name
CDC27
CES5A
MST1P9
refseq
NM_198317
NM_005101
NM_198576
Reference sequence
A
CAG
T
PROBAND: number of reads
with reference
PROBAND : alternative
12
58
0
T
---
A
PROBAND: number of reads
with alternative
14
1
72
Other relative tested (NGS or
Sanger) with the result
Father : absent (exome)
Mother : absent (exome)
Sib II-2: absent (Sanger)
Mutation type
non sense
Father : present
(exome *+ Sanger)
Mother : absent
(exome + Sanger)
Sib II-2: absent
(Sanger)
5-UTR
Father : absent
(exome + Sanger)
Mother : absent
(exome + Sanger)
Sib II-2: absent
(Sanger)
intronic
Mutation : DNA (HGVS
nomenclature _c.)
Mutation : protein (HGVS
nomenclature _p.)
c.549A>T
c.1154+48delCAG
c.329+9T>A
p.Ala182*
Not relevant
unknown
Prediction < SIFT
Damaging
Not predicted
Tolerated
Prediction < PolyPhen-2
Deleterious
-
-
Etc…
Prediction < * (add row per tool)
6.
Discussion. Present arguments as to why and how the candidate genes were selected.
7.
8.
Facultative sections: Acknowledgements, online databases…
References. Maximum 3 references per candidate gene.