Personalis® for Clinical

FAQs

FAQs for Clinicians 2016-12-03T06:23:56+00:00

Frequently Asked Questions

Logistics

How do I contact Personalis’ lab?
Please fill out and submit our Contact Clinical Form and we will respond within two business days. For immediate needs or questions, please call us at +1 650-752-1349.
What is the turnaround time for the ACE Clinical Exome Test?
14 weeks from receipt of sample(s) and all supporting documentation.
What are the sample requirements?
Please go to our Order Information and Sample Logistics page for ordering information and sample requirements.
What types of insurance do you accept?
Personalis performs institutional billing and is also able to accept self-pay; Personalis does not currently accept assignment of benefits from insurers, but can assist with preauthorization requests.
What is the cost of the test?

 

In order to have samples processed in Personalis’ clinical laboratory, you will need to set up an account with us prior to sample submission. Contact our clinical services department at +1 650-752-1349 or clinical@personalis.com to set up an account and inquire about pricing.

Do you perform testing for international providers?
Please contact the Personalis Clinical Operations Team at +1 650-752-1349 or clinical@personalis.com for country specifics.

Sending in Samples

What do I need to do to order a test?
Ordering Checklist:
  • Institutional billing account is established/payment arrangement (P.O., self-pay) is in place.
  • Sample kits provided by Personalis (please contact 650-752-1349 or clinical@personalis.com to request kits).
  • Completed requisition form(s)
[included with each sample].
  • Signed consent form(s) [included with each sample].
  • Medical records, clinic notes, and/or pedigree [included with sample].
  • Patient sample and requisition form submitted in appropriate shipping container(s) with three unique identifiers matching between the form and sample.
  • Family member sample and requisition form submitted in separate shipping container(s) with three unique identifiers matching between the form and sample.
  • Requisition form(s) faxed to +1 650-752-1350 OR emailed via secure email to clinical@personalis.com(if you are emailing requisition forms, please contact us in advance so we may set up the secure email channel).
  • A copy of all paperwork retained by healthcare provider.
  • Is the same requisition form used for proband and family member samples?
    No. The proband’s test requisition form is separate from the family member test requisition form. The family member test requisition includes information linking the family member with the proband. Please submit each form with the relevant sample in a separate bag with three unique identifiers matching between each form and sample. This helps with our tracking and accessioning process. Samples must arrive in a kit with a printed copy of each form (i.e., requisition and consent forms for proband sample, family member requisition/consent form for family member samples). Additionally, please fax the requisition form(s) to +1 650-752-1350 or email via sure email to clinical@personalis.com (if you are emailing requisition forms, please contact us in advance so we may set up the secure email channel).
    What about informed consent forms?
    A signed informed consent form should accompany the proband’s sample. Family members sending in samples sign their own “Family Member” informed consent forms to accompany their samples. A separate signed informed consent form should accompany each sample. The patient/family members should be consented by a genetics professional prior to sample collection. A copy of all paperwork including consent forms should be retained by the healthcare provider.
    Is there any other documentation that I should send in?
    Include paper copies of medical records, clinic note(s), and/or pedigree in the envelope with the sample. The additional clinical information, provided by the clinic note and pedigree, is an integral step to our variant analysis process.

    Reporting

    Do you include the 56 genes as outlined in the American College of Medical Genetics (ACMG) Recommendations for Reporting of Incidental Findings document as part of your report?
    We report “Incidental Findings” for the proband only. Probands may opt in for the reporting of incidental findings in our Informed Consent document. We only report on the genes recommended by the ACMG for incidental findings reporting (but may not report on all depending on IP restrictions).
    How are results reported for family members?
    A report is only issued for the proband. In accordance with ACMG guidelines (Genet Med. 2013 Sep;15(9):733-47), if a variant(s) causative of the clinical phenotype is found in the proband and another family member, the report will indicate that the variant is inherited, but it will not indicate the other family member(s) who also carry the variant. Secondary findings will be analyzed for the proband only, and only if requested on the Informed Consent form (see above).
    If a family member desires testing for a variant identified in the proband, this can be ordered as a separate single-site confirmation test for that family member. Please contact the Personalis Clinical Operations team at +1 650-752-1349 or clinical@personalis.com to arrange.
    If there are two affected siblings in a family, both can be treated as probands with clinical reports being issued for each sibling. Please contact the Personalis Clinical Operations team at +1 650-752-1349 orclinical@personalis.com to arrange.
    Do you report on non-paternity?
    Yes. It is possible that we may learn that the true biological relationships of the family members being tested are different than what has been reported to Personalis. These types of results will be included in the report. This issue is addressed in our Informed Consent form.
    Do you report on consanguinity?
    Yes. We look for unusual levels of homozygosity as this can indicate uniparental disomy or consanguinity, which can guide our analysis. We follow the ACMG guidelines for reporting suspected consanguinity (Genet Med. 2013 Feb;15(2):150-2).
    Do you provide analysis of mitochondrial DNA?
    Yes. We are able to detect and report on variants in the mitochondrial genome.
    Do you report on mosaicism, trinucleotide repeats, or abnormal methylation?
    Currently we do not report on mosaicism, trinucleotide repeats or abnormal methylation. We have detected and reported mosaic variants under a research protocol and are working on clarifying our threshold for clinical reporting. While we do not currently report on abnormal methylation, we do routinely test for some forms of uniparental disomy.
    Do you report “novel” genes not previously associated with human disease?
    In general, we only report genes that have been previously associated with the clinical phenotype of the patient being tested. Occasionally, we will report that the genetic etiology appears to be a variant(s) in a gene that has not been directly implicated in human disease. Very strong evidence must be available for the gene’s likely involvement in such cases, e.g., it may be that the gene lies within a known microdeletion syndrome region which has phenotypic overlap with the case in question, and/or it may be that the gene is already considered a candidate gene for a condition and has strong animal model evidence for the phenotype. In all cases, the report would contain a summary of the evidence for the reported genetic etiology, both at the gene level and at the variant level. All variants in genes that have not been directly implicated in human disease are considered “variants of uncertain significance”.

     

    Can I get the raw data files for my patient?
    Yes. We are happy to provide raw data files (ex. VCF, BAM, FASTQ) to the ordering physician. A separate consent form must be filled out by the physician and all patients submitted as part of the family in order for raw data files to be released. Contact our clinical services department at +1 650-752-1349 orclinical@personalis.com for further information.
    Do you offer re-analysis of data at a later date?
    Yes. Upon physician’s request, we offer re-analysis for a nominal processing fee.

    People

    Who is your clinical laboratory director?
    Dr. Massimo Morra, MD, PhD and Dr. Martina Lefterova, MD, PhD
    Who is on the clinical team working on cases?
    Each case is reviewed by our clinical team, whose members have expertise in in various aspects of genetics/genomics, in order to make thorough assessments regarding the variants that are detected in each sample. Our clinical team comprises lab directors, medical physicians, genetic counselors, PhD scientists, and bioinformaticians.
    Do you have a medical review board?

     

    Personalis has brought together a world-class team of physician scientists with both genomics and clinical expertise, including experts from Stanford University and the University of California, San Francisco (UCSF), to join a leading-edge team of physicians, Ph.D. scientists, genetic counselors, and bioinformaticians at Personalis. This group of experts participates in both the design and development of the ACE Clinical Exome Test as well as the interpretation of submitted cases. The newly formed physician scientist consulting team brings together broad medical genetics expertise with specialists in neurology, cardiology, hereditary cancer, immunology, and dysmorphology.
    Who sits on your scientific advisory board?
    Dr. Michael Snyder, Dr. Atul Butte, Dr. Russ Altman, Dr. Euan Ashley (our founders), and Dr. Carlos Bustamante all sit on our SAB.

    Our Analysis

    How do you measure gene coverage?
    Typical measures of gene coverage such as average depth of coverage for a particular gene can be misleading, as some regions of the gene may have excessive coverage, while other regions are completely missed. In addition, there can be variation in coverage from sample to sample. Therefore we report on the % of exonic bases that reach >20x coverage for each gene as a way to measure if a gene is completely covered at a level that allows for detecting varaints at high sensitivity for variants across the entire gene. For more information, please refer to the ACE Technology section of our website.
    Can I check what the sensitivity to detect variants is for the genes I’m interested in?
    Yes. Please send inquiries to clinical@personalis.com.
    Could you describe your variant analysis process?
    In order to identify the variants most relevant to the patient being sequenced, we take a phenotype-based approach to variant analysis. Instead of relying on blunt filters that exclude variation based on the predicted likelihood of that variant to be disease-causing (e.g., excluding synonymous variants or excluding variants predicted benign by in silico tools such as SIFT and PolyPhen2) we take a rank-based approach that considers the inheritance pattern and presenting phenotype, as well as metrics such as allele frequency and variant type. This has allowed us to reduce the amount of manual review time required to find a causative variant because the best gene/variant/phenotype match is usually at the top of the list.