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Developmental and Neurogenetics Laboratory- Sequencing
Frequently Asked Questions: Whole Exome and Whole Genome Sequencing
1.
What types of patients would benefit from whole exome sequencing or whole genome sequencing
(together referred to as genomic sequencing)?
We have found that testing is useful for patients with rare inherited disorders or with complex clinical
presentations lacking a clear diagnosis. The following criteria can help the provider select cases:
(1) Patient under consideration should be evaluated by physicians with expertise in the patient’s condition to
help the laboratory correlate the patient’s phenotype and family history with the genotype derived from
sequencing. A report from a specialist should be provided to the laboratory when testing is ordered.
(2) The ordering physician should confirm that the patient has had the current standard diagnostic testing
used to evaluate that patient's phenotype to insure that a cost effective approach has been taken to diagnosis.
(3) The provider should choose patients with an apparently undiagnosed monogenic genetic disorder ideally
with a rare or distinctive phenotype, or with a positive family history of multiple affected individuals.
(4) In order to secure insurance pre-authorization the provider should focus on cases where a molecular
diagnosis could help physicians/families with medical decision making/management such as treatment and
family planning. This reasoning should be part of the physician note where testing is recommended
(5) Care should be exercised to select cases where appropriate samples are available to carry out initial
genomic sequencing as well as follow-on testing including confirmatory functional assays in the patient and
segregation analysis of variants in the parents and other family members.
(6) The provider should choose cases where the cost of genomic sequencing appears to be less costly than
testing many individual genes for the phenotype in question.
2.
Test description in plain text:
There are two genomic tests, whole exome sequencing and whole genome sequencing:
Whole exome sequencing determines the DNA sequencing of about 95% of the coding sequences and part of
adjacent introns (non-coding sequences). This represents about 1.5% of the human genome and contains the
part of the genome that is easiest to interpret. In our laboratory, a patient's exome is sequenced to an
average depth of 100X. Over 97% of the exome will be sequenced to a minimum depth of 10X.
Whole genome sequencing determines the sequence of about 95% of the entire genome (coding and noncoding sequences) and is therefore a more complete and more expensive analysis than whole exome
sequencing. In our laboratory, the patient's genome will be sequenced to an average depth of 40X. Over 90%
of the genome will be sequenced to a minimum depth of 10X. The mitochondrial genome of the patient will
be sequenced to a minimum depth of 20X.
3.
Do you report the 57 genes on the ACMG list?
We do not limit our reporting of incidental findings to the 57 gene list.
(https://www.acmg.net/docs/ACMG_Releases_HighlyAnticipated_Recommendations_on_Incidental_Findings_in_Clinical_Exome_and_Genome_Sequencing.pdf).
Human and Molecular Genetics Center
Medical College of Wisconsin
8701 Watertown Plank Rd.
Milwaukee, WI 53226
Phone: 414-955-2550 Fax: 414-955-6516
http://www.hmgc.mcw.edu/
We allow families to choose the categories of incidental findings that they wish to have reported as described
on page 4 of the ‘test request form’ see below. (http://www.hmgc.mcw.edu/forms/DNLSequencingServiceshmgc.pdf)
4.
What is the cost?
This depends on the testing chosen. For details please contact the laboratory at (414)955-2550.
5.
What are the limitations of genomic sequencing?
Exome Limitations:
The whole exome sequence test and associated Sanger sequencing confirmation is designed to evaluate single
nucleotide variants within the human exome. Using this technology it is only possible to sequence 90-95% of
the human reference exome to the minimum 10-fold coverage estimated to be required to reliably detect
heterozygous variants. The ability to identify abnormal variants is dependent on the presence of these
sequence variants in the sequencing data. In addition, certain types of sequence variation are difficult to
identify and have not been validated to be reliably detected for current clinical use. These include insertions,
deletions, copy number variations, long repeat sequences, triplet repeat expansions, structural chromosomal
rearrangements, polyploidy, repetitive regions such as mono-, di- and tri-nucleotide repeats, GC rich regions,
intronic variants outside of the splice-site, and epigenetic effects. The test is limited in its ability to detect
mosaicism. This technology is limited in its ability to accurately identify variants occurring in regions with high
sequence identity to other regions of the genome (e.g. paralogous genes and pseudogenes).
Interpretation assumes that any family relationships stated on the sample submission form are accurate.
Secondary/incidental findings are routinely confirmed by Sanger sequencing in the proband only, but can be
provided upon request for the parents (applies to trio analysis).
Variants found in a patient that are benign based on the medical literature, have an allele frequency greater
than or equal to 1%, result in a synonymous amino acid change or occur in 5’ or 3’ untranslated regions are
generally not reported, but may be made available on request.
Normal findings do not rule out the diagnosis of genetic abnormalities. If specific clinical disorders are
suspected, specific evaluation of known genes by alternate test methods should be considered. Variants that
interfere with DNA sequencing and medical procedures such as bone marrow transplantation and blood
transfusion may result in misleading results. The clinical implications of certain variants may be unknown at
the time of analysis. At the present time, the laboratory does not report variants found in the mitochondrial
genome.
Whole Genome Limitations:
The Whole genome sequencing test and associated Sanger sequencing confirmation are designed to evaluate
single nucleotide variants within the human genome. Using this technology it is only possible to sequence 9095% of the human reference genome to the minimum 10-fold coverage estimated to be required to reliably
detect heterozygous variants. The ability to identify abnormal variants is dependent on the presence of these
sequence variants in the sequencing data. In addition, certain types of sequence variation are difficult to
identify and have not been validated to be reliably detected for current clinical use. These include insertions,
deletions, copy number variations, long repeat sequences, triplet repeat expansions, structural chromosomal
rearrangements, polyploidy, repetitive regions such as mono-, di- and tri-nucleotide repeats, GC rich regions,
intronic variants outside of the splice-site, and epigenetic effects. The test is limited in its ability to detect
mosaicism. This technology is limited in its ability to accurately identify variants occurring in regions with high
sequence identity to other regions of the genome (e.g. paralogous genes and pseudogenes).
Interpretation assumes that any family relationships stated on the sample submission form are accurate.
Secondary/incidental findings are confirmed by Sanger sequencing in the proband only.
Variants found in a patient that are benign based on the medical literature, have an allele frequency greater
than or equal to 1%, result in a synonymous amino acid change, occur in 5’ or 3’ untranslated regions, occur
between genes or in intronic regions outside of the canonical splice site are not generally reported but may be
made available on request.
Normal findings do not rule out the diagnosis of genetic abnormalities. If specific clinical disorders are
suspected, specific evaluation of known genes by alternate test methods should be considered. Variants that
interfere with DNA sequencing and medical procedures such as bone marrow transplantation and blood
transfusion may result in misleading results. The clinical implications of certain variants may be unknown at
the time of analysis. At the present time, the laboratory does not report variants found in the mitochondrial
genome.
6.
How do I order?
Details concerning testing ordering and billing can be found at the laboratory website:
http://www.hmgc.mcw.edu/clinical/index.htm
7.
How do I get counseling for my patient?
Genetic counseling concerning genomic sequencing is available at all major medical centers around the United
States. We can help you find a genetic counselor in your area.
8.
How do I get access to data?
The laboratory will provide patients with a copy of the patient’s genomic data in the VCF format on a hard
drive for a small fee (written patient consent required).
9.
Can data be shared with other providers?
Upon receipt by the laboratory of written patient consent to do so, the data provided by the laboratory can be
shared by the patient with a provider(s) at their discretion. The laboratory will provide a copy of the patient’s
genomic data in the VCF format on a hard drive for a small fee (written patient consent required).
10. How will data be reported in the medical record?
A laboratory report that includes primary findings (those DNA changes related to the patient’s medical
condition) and secondary or incidental findings requested by the patient or the patient’s parents/legal
guardians will be returned to the ordering provider for integration into the patient’s medical record.
11. Are specimen collection kits available?
The laboratory can provide a sample collection kit if requested.
12. What if there is a specific gene(s) I am interested or concerned about?
For details please contact the laboratory at 414-955-2550.
13. Who will have access to data not reported?
Only the laboratory has access to the data used to generate the report. The laboratory will provide patients
with a copy of the patient’s genomic data in the VCF format on a hard drive for a fee.
14. How long are patient samples and data stored?
DNA samples and genomic data are stored in accordance with Wisconsin law (currently requires storage of
data for 3 years).
15. Will samples yielding a negative test result be reanalyzed?
The laboratory is able to reanalyze a patient’s previous genomic data at the request of a physician. Data
analysis test fees will apply.
16. Do you perform research on samples/data?
Research is only performed on a sample with the patient’s or patient’s parents/guardian’s permission and
signed written consent.

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