Molecular Genetics Requisition Form 2. Clinical Whole Exome Sequencing Informed Consent 5. Clinical Whole Exome Sequencing Information & FAQ 12

Transcription

1 NYGC CLINICAL WHOLE EXOME SEQUENCING Phone: Fax: TABLE OF CONTENTS Molecular Genetics Requisition Form 2 Clinical Whole Exome Sequencing Informed Consent 5 Clinical Whole Exome Sequencing Information & FAQ 12 Clinical Sample Submission Guidelines for Constitutional Testing 17 1

2 MOLECULAR GENETICS REQUISI TION FORM Proband Information (print or affix label) Last name First name Street address Ethnicity (check all that apply) African-American Caucasian Hispanic Ashkenazi Jewish Middle Eastern Other Ordering Physician City State, Zip Code, Country Last name First name Date of Birth (MM/DD/YYYY) Hospital MRN/Patient identifier National Provider Identifier number (NPI) Gender: Male Female Unknown Test Requested Whole Exome Sequencing Clinical Information Complete page 2, provide clinic notes and pedigree Indication for test: ICD-10 code(s): Proband Sample Information Collection date Phone Blood (2-5mL in lavender top EDTA tube) DNA (>5 µg, at least 50ng/ul extracted in a clinical lab) Saliva (2mL in OrageneDx Collection Kit) Other (call before sending) Family Member Samples Please call the laboratory before sending more than 3 family samples or if samples from both biological parents are not available. Note: A separate report will not be issued for family member samples. Mother Last name Date of birth (MM/DD/YYYY) Collection date Father Whole Genome Sequencing Collection time First name Blood Affected Yes No DNA Enclosed Yes No Saliva Institution Street Address City Phone address Additional Report Physician/Genetic Counselor State, Zip Code, Country Fax National Provider Identifier number (NPI) Institution Phone address Confirmation of Informed Consent By ordering testing, the undersigned person represents that he/she is a licensed medical professional authorized to order genetic testing and acknowledges that the patient has been supplied information regarding genetic testing and has given consent for this genetic test to be performed in accordance with New York Civil Rights Law 79-L. Provider name Fax Provider signature Last name Date of birth (MM/DD/YYYY) Collection date Collection time Additional Relative (relationship): Last name Date of birth (MM/DD/YYYY) Collection date Collection time First name Blood Affected Yes No DNA Enclosed Yes No Saliva First name Blood Affected Yes No DNA Enclosed Yes No Saliva Ordering Check List All must be provided before testing may begin Patient information form (page 1) Clinical information (page 2) Payment information (page 3) Informed consent Clinical notes, number of pages: Pedigree Specimen(s) labeled with name and DOB or MRN Date/time received: Received by: MRN: LAB USE ONLY Container/specimen type: Sample Volume: Sample IDs: 2

3 CLINICAL WHOLE EXOME SEQUENCING REQUISITON Perinatal History Craniofacial/ Hematologic/Immunologic Prematurity Ophthalmologic/Auditory Anemia Intrauterine growth restriction (IUGR) Macrocephaly Neutropenia Oligohydramnios Microcephaly Pancytopenia Polyhydramnios Cleft lip/palate Autoimmune disease Cystic hygroma Craniosynostosis Other: Other: Abnormal philtrum Mid-face hypoplasia Gastrointestinal Growth Irregular teeth Jaundice Failure to thrive Cataracts Gastroschisis Short stature Coloboma Omphalocele Overgrowth Ptosis Anal atresia Other: Strabismus Tracheoesophageal fistula Blindness Hepatomegaly Cognitive Ear tags/pits Pyloric stenosis Developmental delay Microtia Other: Fine motor External ear malformation Gross motor Hearing loss Endocrine Speech Deafness Diabetes mellitus Intellectual disability/mr Facial dysmorphism describe: Type I Type II IQ: Hypothyroidism Developmental regression Other: Hypoparathyroidism Other: Cardiac Genitourinary Behavioral/Psychiatric Atrial septal defect (ASD) Ambiguous genitalia Autism Ventricular septal defect (VSD) Hypospadias Autism spectrum disorder Coarctation of the aorta (COA) Cryptorchidism Hyperactivity Hypoplastic left heart syndrome (HLHS) Kidney malformation Anxiety Tetralogy of Fallot (TOF) Renal agenesis Other: Transposition of the Great Arteries (TGA) Hydronephrosis Cardiomyopathy Musculoskeletal Other: Previous Genetic Testing Club foot Single gene test or gene panel Diaphragmatic hernia Neuromuscular Mitochondrial testing Polydactyly Ataxia Karyotype and/or FISH Clinodactyly Chorea Chromosomal microarray Syndactyly Exercise intolerance Other (specify) Clenched hands Fatigue No prior testing Rocker bottom foot Headaches/migraines Contractures Dystonia Other relevant clinical Scoliosis Hypotonia or research info Other: Hypertonia Neuropathy (include any suspected genes and/or inheritance patterns): Brain anomalies Seizures Dandy-Walker malformation Type: Holoprosencephaly Lissencephaly Agenesis of the corpus callosum Hydrocephalus Other: Other: Metabolic Ketosis Lactic acidosis Organic aciduria Other: 3

4 CLINICAL WHOLE EXOME SEQUENCING REQUISITON Institutional Billing Institution name Institution code Billing address City State and Zip Code Billing contact Contact phone number Fax number Send copy of report Institutional financial policy: The institution accepts full financial responsibility of for the full price of the test. Please sign and date below if you are an agent of the ordering financial institution and can authorize payment for this test. I have read and agree to the institutional billing policy. Printed name Signature Date Credit Card Payment Visa Master Card Discover American Express Cardholder s name Card number Expiration date CVV code Billing address City State and Zip Code I hereby authorize NYGC to bill my credit card as indicated above. Printed name Signature Date 4

5 CLINICAL WHOLE EXOME SEQUENCING INFORMED CONSENT PLEASE NOTE: This consent document provides information about the clinical whole exome sequencing test. It is meant to supplement discussions with a physician and/or genetic counselor regarding the purpose, benefits, risks and limitations of the test. If you are the parent/guardian of a child under the age of 18 being referred for this test, the words you, your and my refer to your child throughout the entire document. If you choose to proceed with testing for your child after reading this document, you will be asked to sign this document on behalf of your child to indicate consent for testing. If you are over 18 and are the individual being referred for this test, the word you refers to you throughout the entire document. If you choose to proceed with testing after reading this document, you will be asked to sign this document to indicate your consent for testing. DESCRIPTION OF WHOLE EXOME SEQUENCING Your provider has ordered whole exome sequencing (WES) because you have a medical condition that may have an underlying genetic cause or you wish to learn your risk of developing a genetic condition and/or having a child with a genetic condition. Due to the complexity of this test, we recommend you seek genetic counseling from a physician and/or certified genetic counselor both before and after testing. After reading this document and consulting with your physician and/or genetic counselor, if you agree to have WES performed on your DNA sample, please sign this document on page 6. A copy of this consent document will be provided to you for your records. WES is a complex genetic test that involves sequencing the regions of the genome that contain the functionally important sequences of DNA. Individually, these regions are referred to as exons. Together, the exons are referred to as the exome and comprise approximately 1% of our DNA. An estimated 85% of disease causing, or pathogenic, genetic changes occur within the exome. Unlike other tests that sequence one or a few genes at a time, WES examines thousands of genes at the same time. Therefore, this test has a higher likelihood of finding the cause of your condition than other genetic tests you may have had. DNA samples from you and other family members are needed for this test. Approximately two teaspoons of blood will be drawn and sent to the laboratory, where DNA will be extracted from the blood and prepared for sequencing. Your exome will be sequenced and compared to the exome sequence of your family members and the normal reference sequence. The normal reference sequence is DNA from individual(s) that do not have any known disease. Differences between your exome sequence and the exome sequence of your unaffected family members and the normal reference sequence are called sequence variants. These sequence variants will be filtered using a system developed by NYGC. Then, a board certified clinical laboratory director will interpret the relevance of the sequence variants based on the clinical symptoms and medical history your doctor has provided to NYGC. The entire test takes approximately 12 weeks to complete. Interpretation of the WES test is dependent on a complete and accurate report of your reason for testing. For this reason, we ask your physician to provide detailed medical records documenting your medical history, current diagnosis and family history. Please initial below to consent to your provider sharing this information with NYGC. (Initial) My provider may share clinical notes and medical records detailing my current diagnosis, family history, and medical history, which may include the results of previous genetic tests, with NYGC to help guide the interpretation of my WES test. 5

6 CLINICAL WHOLE EXOME SEQUENCING INFORMED CONSENT REQUEST FOR SAMPLES FROM FAMILY MEMBERS Each WES test generates hundreds of thousands of variants. Samples from biological parents and/or other relatives are necessary to facilitate the filtering of the variants through co-segregation (family study) analyses. Analyzing sequencing data for variants that occur in your DNA but not in your parents or other relatives may help identify new, or de novo, variants that may be causing your condition. Providing samples from family members increases the likelihood of identifying the genetic cause of your condition and decreases the likelihood of uncertain or unclear results. WES and any confirmatory testing required to interpret your results will be completed on your family members samples. No other testing will be performed and results will not be provided for individual family member samples. However, inheritance information for your relatives may be provided for variants detected and reported for your sample. This information will be included in your report and the names of your family members will not be used. Variants are filtered based on their presence in your sample and therefore variants present only in family members and not in your sample will not be detected or reported. Family members wishing to undergo genetic testing for their own medical management should discuss testing options with a physician or genetic counselor. Family members must initial below to consent to inheritance information being included on your report. Consent will not be implied if this section is left blank. (Initial) Mother: NYGC may indicate if variants detected and reported in my child s sample were inherited. I understand that this information will be included on their report and my name will not be used. (Initial) Father: NYGC may indicate if variants detected and reported in my child s sample were inherited. I understand that this information will be included on their report and my name will not be used. (Initial) Additional relative: NYGC may indicate if I have also inherited variants detected and reported in my relative s sample. I understand that this information will be included on their report and my name will not be used. VARIANT REPORTING A single report will be issued containing your test results. The report will include all variants that may be contributing to your reported condition. Variants will be classified according to American College of Medical Genetics and Genomics (ACMG) practice guidelines. All reported variants will be confirmed by an alternative method such as Sanger sequencing. The different types of reported variants are defined in the table on page 3. The finding of a pathogenic variant does not predict the onset, severity, or spectrum of your condition. It is possible that no pathogenic variants are found and the genetic cause of your condition is not identified by WES. A negative test result may reduce the likelihood that your condition is genetic but does not eliminate the possibility. A negative test result does not change the diagnosis your physician has given you. Additional testing may be recommended. 6

7 CLINICAL WHOLE EXOME SEQUENCING INFORMED CONSENT Variant Type Pathogenic Likely pathogenic Variant of uncertain clinical significance (VOUS) Secondary finding Description Previously identified variant known to be disease causing and related to the patient s phenotype High certainty that the variant is disease causing based on available literature Unknown, uncertain, or conflicting literature about the pathogenicity of the variant Known pathogenic variant in a gene not related to the patient s phenotype but included in the ACMG-56 list or associated with an autosomal recessive condition recommended for reproductive carrier screening SECONDARY FINDINGS WES may identify incidental or secondary findings that are not related to the reason you are having the test. The ACMG has developed guidelines for the reporting of secondary findings. The guidelines include a list, which may be updated periodically, of 56 medically actionable genes for which secondary findings should be sought and reported regardless of the reason for testing. The current ACMG policy statement on secondary findings may be viewed in its entirely online (PubMed ID: ) and the list of 56 genes is provided for your reference in our WES FAQ document. NYGC will report pathogenic variants in these genes by default unless you decline this option. You should discuss the details of the genes and associated genetic conditions included in the ACMG list as well as the risks, benefits, and limitations of receiving secondary findings from your WES with your physician and/or genetic counselor. You must initial below to opt-out of the reporting of secondary findings. (Initial) I choose NOT to receive secondary findings from my WES. CARRIER STATUS FOR AUTOSOMAL RECESSIVE CONDITIONS WES may identify pathogenic variants in genes associated with autosomal recessive conditions but unrelated to your clinical symptoms. For autosomal recessive conditions, both copies of the gene (maternal and paternal) must contain the pathogenic variant in order to cause disease. An individual with a pathogenic variant in only one copy of the gene does not show symptoms of disease and is referred to as a carrier. You may choose to have NYGC report known pathogenic variants in genes recommended by the ACMG and the American Congress of Obstetricians and Gynecologists (ACOG) for reproductive carrier screening. A list of the genes can be found in our WES FAQ document. However, WES is not designed to be a comprehensive carrier screen and NYGC cannot guarantee that carrier status will always be determined. Some genes associated with autosomal recessive conditions may have little or no coverage by WES. Carrier testing for reproductive purposes should be discussed with your physician and/or genetic counselor. You must initial below to opt-in to the reporting of carrier status for autosomal recessive conditions. (Initial) I want NYGC to report known pathogenic variants in genes associated with select autosomal recessive conditions but unrelated to my clinical symptoms. 7

8 CLINICAL WHOLE EXOME SEQUENCING INFORMED CONSENT OTHER FINDINGS Most variants not related to the condition for which you are having WES will not be reported. This includes variants that are predicted to be benign, variants unrelated to your reported medical condition (with the exception of variants in genes on the ACMG list and genes involved in select autosomal recessive conditions), variants that have been found in research studies to be associated with a small increase or decrease risk to develop common disorders (e.g. heart disease or diabetes) and variants that increase the risk for disease that might occur at an advance age (e.g. Alzheimer s Disease) for which there is no prevention or treatment. RISKS ASSOCIATED WITH WHOLE EXOME SEQUENCING This test may not generate accurate results in instances that cannot be predicted. Such instances include but are not limited to: incomplete medical and/or family history, unavailability of critical family members for co-segregation analysis, technical problems, inaccurate reporting of family relationships, or technical problems. This test may suggest that biological relationships of family members are not as reported, such as non-paternity (the individual identified as the father of the child is not the biological father). NYGC will not state relationship discrepancies in your test report. This test may reveal pathogenic variants unrelated to the reason why WES was ordered, you decide whether or not to receive these types of findings. The results of this test may have significant medical, psychological, and social implications for you and your family. You and your family members may experience anxiety before, during, and after testing. LIMITATIONS OF WHOLE EXOME SEQUENCING Current WES techniques may not be able to capture, or target, the entire exome. Approximately 10% of the exons that are targeted may not have enough coverage (produce enough data) for analysis. A list of genes that are undercovered is available upon request. Certain types of DNA changes cannot be detected by current WES technology. There is a possibility that WES may not detect a variant that is the cause of your condition. WES is performed and the findings are reported based on current medical knowledge. Some of the variants that are identified by WES cannot be definitively classified. In some cases, testing of additional family members may provide additional information. In other cases, the significance of the variant will remain unknown until additional scientific research is available. If you are undergoing WES to learn your risk of developing a genetic condition and/or having a child with a genetic condition, the laboratory reserves the right to only report secondary findings in medically actionable genes on the ACMG list and carrier status for autosomal recessive conditions. If you opt-out of secondary findings and do not optin to carrier status, your specimen will be rejected and your physician will be notified. 8

9 CLINICAL WHOLE EXOME SEQUENCING INFORMED CONSENT SPECIMEN RETENTION Without specific, signed authorization, no additional clinical testing will be performed on this sample. The original specimen and any products derived from them (i.e. DNA) will be destroyed after testing is completed or no more than 60 days after results are reported to the ordering physician. However, NYGC can store your DNA for a longer period of time to enable additional testing in the future without having to obtain a new sample. You must initial below to authorize the laboratory to retain your sample for this purpose. Consent to specimen retention will not be implied if this section is left blank. (Initial) Proband: I want NYGC to store my DNA sample for 2 years after results are reported to my physician. I understand that my sample will be destroyed after this time if no additional testing is ordered. (Initial) Mother: I want NYGC to store my DNA sample for 2 years after results are reported to my child s physician. I understand that my sample will be destroyed after this time if no additional testing is ordered. (Initial) Father: I want NYGC to store my DNA sample for 2 years after results are reported to my child s physician. I understand that my sample will be destroyed after this time if no additional testing is ordered. (Initial) Additional relative: I want NYGC to store my DNA sample for 2 years after results are reported to my relative s physician. I understand that my sample will be destroyed after this time if no additional testing is ordered. FINANCIAL RESPONSIBILTY (Initial) I understand that I am responsible for the cost of the WES test and will be required to pay for any/ all of the test cost not paid by my health insurance. AUTHORIZATION FOR VOLUNTEER PARTICIPATION IN RESEARCH After all testing is completed, NYGC would like to store de-identified samples and raw sequencing data from you and your family members for test validation, research, education, and other purposes. You must initial below to consent to NYGC retaining and using your de-identified samples and raw data for these purposes. Consent to specimen retention for research will not be implied if this section is left blank. (Initial) Proband: NYGC may retain and use my de-identified samples and raw sequencing data indefinitely for test validation, research, education, and other purposes. (Initial) Mother: NYGC may retain and use my de-identified samples and raw sequencing data indefinitely for test validation, research, education, and other purposes. 9

10 CLINICAL WHOLE EXOME SEQUENCING INFORMED CONSENT (Initial) Father: NYGC may retain and use my de-identified samples and raw sequencing data indefinitely for test validation, research, education, and other purposes. (Initial) Additional relative: NYGC may retain and use my de-identified samples and raw sequencing data indefinitely for test validation, research, education, and other purposes. In order to improve diagnostic testing and build upon our understanding of the relationship between genetic variants and clinical symptoms, we would like to enter de-identified clinical information and sequencing data from you and your family members into an internal database maintained by NYGC. The database is used to track variants that are present in healthy and diseased individuals with hopes of discovering which variants may be causing or contributing to disease. This database of de-identified clinical and sequencing data may be accessed by investigators at NYGC, investigators at other institutions, and other partners who are interested in studying gene variants. This may include partners involved in the development of products of commercial value. Should such products be developed, you would not share their financial value. In addition, information from this internal database may be uploaded to public NIH databases such as ClinVar, dbvar, or dbgap. The identities of patients and family members are never disclosed to any database and the data does not contain any names or other identifiable information that can link it back to the individual. Although you will not directly benefit from database reporting, others may benefit in the future. You may opt-out of database reporting by initialing below, calling your physician/genetic counselor, or calling the laboratory. If you do not opt-out by one of these methods, your data will be de-identified and used. (Initial) Proband: I do NOT authorize NYGC to submit my de-identified clinical information and sequencing data to internal and public databases. (Initial) Mother: I do NOT authorize NYGC to submit my de-identified clinical information and sequencing data to internal and public databases. (Initial) Father: I do NOT authorize NYGC to submit my de-identified clinical information and sequencing data to internal and public databases. (Initial) Additional relative: I do NOT authorize NYGC to submit my de-identified clinical information and sequencing data to internal and public databases. 10

11 CLINICAL WHOLE EXOME SEQUENCING INFORMED CONSENT CONSENT FOR WHOLE EXOME SEQUENCING PROBAND (INDIVIDUAL SEEKING TESTING) I have read the consent form and my signature below attests that my physician and/or genetic counselor has reviewed with me the purpose, benefits, risks and limitations of WES to my satisfaction and I would like NYGC to perform WES on my DNA sample. Proband Name (please print): Name of parent, guardian, or representative giving consent (if applicable): Signature: Date: MOTHER I understand that I am submitting my sample to help guide the interpretation of my child s test results. I understand that a report will not be issued for my sample and that if I want to receive results for my sample, I will need to be tested separately. Name (please print): Signature: Date: FATHER I understand that I am submitting my sample to help guide the interpretation of my child s test results. I understand that a report will not be issued for my sample and that if I want to receive results for my sample, I will need to be tested separately. Name (please print): Signature: Date: ADDITIONAL RELATIVE I understand that I am submitting my sample to help guide the interpretation of my relative s test results. I understand that a report will not be issued for my sample and that if I want to receive results for my sample, I will need to be tested separately. Name (please print): Signature: Date: PHYSICIAN OR GENETIC COUNSELOR OBTAINING CONSENT I have discussed the purpose, benefits, risks and limitations of WES with the patient/parent/ guardian and my signature below affirms that I have offered genetic counseling and I accept the responsibility of the post-test genetic counseling for this patient/family. Name (please print): Signature: Date: 11

12 CLINICAL WHOLE EXOME SEQUENCING INFORMATION & FAQ WHAT IS WHOLE EXOME SEQUENCING? Whole exome sequencing, or WES, is a complex genetic test that involves sequencing the regions of the genome that contain the functionally important sequences of DNA. Individually, these regions are referred to as exons. Together, the exons are referred to as the exome and comprise approximately 1% of our DNA. An estimated 85% of disease causing, or pathogenic, genetic changes occur within the exome. WHEN IS WES USEFUL? WES may be the best genetic test to identify the molecular genetic cause of a patient s condition in the following cases: The patient has had comprehensive targeted genetic testing and the molecular genetic cause has not been identified. The patient is suspected to have a genetic condition that is associated with many different genes and no single gene or group of genes makes up a significant percentage of the molecular cause. The patient has a constellation of features that is suspicious of a genetic condition but does not fall within a specific recognized syndrome. The patient has a constellation of features that is associated with multiple differential diagnoses. The patient is a healthy adult over the age of 18 who is interested in learning about his or her risk to develop genetic conditions with available screening, treatment or other intervention and/or carrier status for select autosomal recessive conditions. HOW IS WES PERFORMED? The exome is targeted, captured and sequenced for the patient and family member samples. The sequence of the affected individual(s) is compared to the sequence of the other family members and to the normal reference sequence. The reference sequence is the DNA sequence from individual(s) who do not have any known disease. Differences in DNA sequence between the affected patient (the proband) and unaffected family members and the reference sequence are called sequence variants. Sequence variants are filtered using various stringencies as part of a proprietary pipeline developed by NYGC that incorporates variant databases and disease-specific databases. Then, the clinical laboratory director will interpret the relevance of the filtered variants based on the clinical symptoms and medical history your doctor has provided to NYGC. HOW LONG DOES WES TAKE? A report is usually issued within 12 weeks of initiation of the test. Testing may be delayed if not all family samples are received together, a complete medical history is not provided, or if insurance pre-authorization must be completed before the test is initiated. WHAT TYPES OF SAMPLES CAN BE SUBMITTED FOR WES? Blood: 5ml of whole blood in an EDTA (lavender top) tube. Purified DNA: High quality (min. 50ng/ul) DNA extracted in a clinical laboratory can be accepted. At least 5µg is needed. 12

13 CLINICAL WHOLE EXOME SEQUENCING INFORMATION & FAQ Saliva: 2mL of saliva in a saliva collection tube provided in OrageneDx Collection Kit. Other tissue types: On a case-by-case basis. Please call to discuss an individual case. Fetal DNA will only be accepted from pregnancies that are not continuing due to fetal demise or termination. Post-mortem samples will be accepted in the forms indicated above. Samples fixed in formalin will not be accepted. WHY DOES NYGC ASK FOR SAMPLES FROM FAMILY MEMBERS FOR WES? WES generates hundreds of thousands of variants. Samples from biological parents and other relatives are necessary to facilitate the filtering of the variants through co-segregation (family study) analyses. Providing samples from family members increases the likelihood of identifying the genetic cause of your condition and decreases the likelihood that variants identified during WES will remain of uncertain significance. When the proband is the only affected person in the family, a sample from the patient and both biological parents is preferred. Please contact NYGC for guidance on the best family member samples to provide for a particular case. DOES NYGC ACCEPT SAMPLES FROM MORE THAN THREE FAMILY MEMBERS? Yes. In families where multiple family members are suspected to have the same condition, NYGC will accept samples from affected family members for co-segregation analysis. Clinical notes documenting the family member s diagnosis should be provided. Results will not be provided for family member samples. The proband s report will indicate if a variant detected and reported was inherited. However, the report will not identify the family member from which the variant was inherited. Family members wishing to undergo genetic testing for their own medical management should discuss testing options with a physician or genetic counselor. WILL NYGC PERFORM WES WITHOUT SAMPLES FROM FAMILY MEMBERS? Yes. If only the proband s sample is available, NYGC will still perform WES. However, there are limitations of the test including a decreased likelihood of identifying the molecular genetic cause of the proband s reported phenotype and an increased likelihood of identifying variants of uncertain significance. Additionally, analysis of novel genes will not be performed without parental samples. DOES NYGC ACCEPT SAMPLES SENT DIRECTLY BY PATIENTS? No. WES can only be ordered by and reported to a healthcare provider. The results of this test will be sent electronically to the ordering physician and/or genetic counselor and may become a part of the proband s medical record. WHY DOES NYGC NEED DETAILED CLINICAL INFORMATION FOR WES? Analysis and interpretation of WES data is dependent on accurate knowledge of the proband s complete phenotype and medical history. For this reason, it is critical to provide detailed clinic notes, imaging studies, a pedigree, and any other information related to the proband s medical condition. 13

14 CLINICAL WHOLE EXOME SEQUENCING INFORMATION & FAQ WHAT TYPES OF FINDINGS DOES A WES REPORT CONTAIN? A single report will be issued for the proband. Variants will be classified according to guidelines developed by the American College of Medical Genetics and Genomics (ACMG). All reported variants will be confirmed by an additional method, such as Sanger sequencing. Reports may include one or more of the following variant types: Variant Type Pathogenic Likely pathogenic Variant of uncertain clinical significance (VOUS) Secondary finding Description Previously identified variant known to be disease causing and related to the patient s phenotype High certainty that the variant is disease causing based on available literature Unknown, uncertain, or conflicting literature about the pathogenicity of the variant Known pathogenic variant in a gene not related to the patient s phenotype but included in the ACMG-56 list or associated with an autosomal recessive condition recommended for reproductive carrier screening Reports are always sent to the referring provider(s). In accordance with federal law, patients may submit a written request for a copy of their test results. However, given the complex nature of clinical whole exome sequencing, NYGC strongly recommends that patients obtain copies of their reports from their physician or genetic counselor. WILL NYGC REPORT VARIANTS THAT ARE NOT ASSOCIATED WITH THE PATIENT S REPORTED CLINICAL SYMPTOMS? Yes. The ACMG has compiled a list of 56 medically actionable genes for which pathogenic variants should be sought and reported regardless of the indication for WES. The current ACMG policy statement on secondary findings may be viewed in its entirely online (PubMed ID: ). For reference, the list of 56 genes is provided on page 4 of this FAQ document. This list may be updated periodically to reflect changes in the ACMG guidelines. Patients must opt-out on the WES consent form to decline the reporting of secondary findings. In addition, patients may opt-in to receive information regarding carrier status for autosomal recessive conditions recommended for reproductive carrier screening. NYGC will attempt to report known pathogenic variants in genes on the ACMG list and genes associated with autosomal recessive conditions for patients that choose to receive this information. NYGC cannot guarantee that all exons of all the genes will be well covered by WES. ARE THERE ANY FINDINGS THAT WON T BE REPORTED? Yes. Most variants not related to the proband s reported phenotype will not be reported. The following types of variants will not be reported: Pathogenic variants unrelated to the proband s phenotype (unless present in a gene on the ACMG list or a gene associated with autosomal recessive disease). Variants that are predicted to be benign or likely benign. Variants that have been found in research studies to be associated with a small increase or decrease in risk for common disorders (e.g. heart disease or diabetes). 14

15 CLINICAL WHOLE EXOME SEQUENCING INFORMATION & FAQ Variants that increase the risk for a disease that might occur at an advance age (e.g. Alzheimer s Disease) for which there is no prevention or treatment. WES may reveal that the biological relationships of the family members being tested have been reported incorrectly. For example, non-paternity, or that the individual identified to be the father of a child is not the biological father. This information will not be explicitly reported but may be inferred from the test report. ARE THERE ANY PATHOGENIC VARIANTS THAT ARE NOT DETECTED BY WES? Yes. Certain types of pathogenic variants cannot be detected by current WES technology, including: Large copy number variants Methylation abnormalities Variants in genes with highly homologous pseudogenes Expansions of trinucleotide repeats Variants with low levels of mosaicism Variants confounded by various non-mendelian factors (penetrance, variable expressivity, multifactorial disease, epigenetic factors, phenocopies and uniparental disomy) Variants in regions of the exons that are not well covered by WES ARE THERE GENES THAT ARE NOT WELL COVERED BY WES? Yes. Not all exons in the genome are targeted and captured. Approximately 10% of the exons that are targeted for WES may not be well covered. Information about how much of the exome was evaluated will be included in the report. The empirical coverage data for all or specific genes can be requested from NYGC. WILL NYGC EXAMINE NOVEL GENES? Sometimes. If both parents are submitted with the proband s sample and there are no variants related to the proband s reported phenotype in characterized genes, novel genes will be evaluated and candidate gene variants will be reported. WILL NYGC PROVIDE SEPARATE REPORTS FOR FAMILY MEMBER SAMPLES? No. Family member samples are used for the interpretation of the proband s test results only. While WES will be completed on two or more family member samples, the data will only be analyzed for co-segregation of variants identified in the patient. Reports will not be issued for family members, but inheritance information may be included on the proband s report if requested. WHAT IF EXTENDED FAMILY MEMBERS WANT TO BE TESTED? Extended family members may be tested for the pathogenic variants identified in the proband. There is a separate cost for this test. Please see our targeted variant testing requisition form for details. 15

16 CLINICAL WHOLE EXOME SEQUENCING INFORMATION & FAQ WHAT SEQUENCING PLATFORM IS USED FOR WES? Exome capture is performed via the Agilent SureSelect XT Human All Exon V5+UTRs target enrichment kit. The captured exome is sequenced on an Illumina HiSeq 2500 with 125 basepair (bp) paired-end reads. WHAT IS THE COVERAGE OF WES? This test is designed to capture 71 million bases (out of total 3 billion) of the genome. At least 90% of the targeted region is covered at read depth of 20x or greater. Table 1: Autosomal Recessive Carrier Status Conditions and Genes Gene Condition Gene Condition ASPA Canavan disease HBB Sickle cell anemia BLM Bloom syndrome HEXA Tay-Sachs disease CFTR Cystic fibrosis IKBKAP Familial dysautonomia FANCC Fanconi anemia group C MCOLN1 Mucolipidosis IV GBA Gaucher disease Type 1 SMPD1 Niemann-Pick type A Table 2: ACMG List of Conditions and Genes for Return of Secondary Findings in Clinical WES Gene Condition Gene Condition APC Adenomatous polyposis coli TGFBR2 Loeys-Dietz syndrome type 1B MYH11 Aortic aneurysm, familial thoracic 4 TGFBR1 Loeys-Dietz syndrome type 2A ACTA2 Aortic aneurysm, familial thoracic 6 TGFBR2 Loeys-Dietz syndrome type 2B MYLK Aortic aneurysm, familial thoracic 7 SMAD3 Loeys-Dietz syndrome type 3 TMEM43 Arrhythmogenic right ventricular cardiomyopathy, type 5 KCNQ1 Long QT syndrome 1 DSP Arrhythmogenic right ventricular cardiomyopathy, type 8 KCNH2 Long QT syndrome 2 PKP2 Arrhythmogenic right ventricular cardiomyopathy, type 9 SCN5A Long QT syndrome 3 DSG2 Arrhythmogenic right ventricular cardiomyopathy, type 10 MLH1 Lynch syndrome DSC2 Arrhythmogenic right ventricular cardiomyopathy, type 11 MSH2 Lynch syndrome BRCA1 Breast-ovarian cancer, familial 1 MSH6 Lynch syndrome BRCA2 Breast-ovarian cancer, familial 2 PMS2 Lynch syndrome SCN5A Brugada syndrome 1 RYR1 Malignant hyperthermia RYR2 Catecholaminergic polymorphic ventricular tachycardia CACNA1S Malignant hyperthermia LMNA Dilated cardiomyopathy 1A FBN1 Malignant hyperthermia MYBPC3 Dilated cardiomyopathy 1A TGFBR1 Marfan's syndrome COL3A1 Ehlers-Danlos syndrome, type 4 MEN1 Multiple endocrine neoplasia, type 1 GLA Fabry's disease RET Multiple endocrine neoplasia, type 2a APOB Familial hypercholesterolemia RET Multiple endocrine neoplasia, type 2b LDLR Familial hypercholesterolemia MUTYH MYH-associated polyposis MYH7 Familial hypertrophic cardiomyopathy 1 NF2 Neurofibromatosis, type 2 TPM1 Familial hypertrophic cardiomyopathy 3 SDHD Paragangliomas 1 MYBPC3 Familial hypertrophic cardiomyopathy 4 SDHAF2 Paragangliomas 2 PRKAG2 Familial hypertrophic cardiomyopathy 6 SDHC Paragangliomas 3 TNNI3 Familial hypertrophic cardiomyopathy 7 SDHB Paragangliomas 4 MYL3 Familial hypertrophic cardiomyopathy 8 STK11 Peutz-Jeghers syndrome MYL2 Familial hypertrophic cardiomyopathy 10 MUTYH Pilomatrixoma ACTC1 Familial hypertrophic cardiomyopathy 11 PTEN PTEN hamartoma tumor syndrome RET Familial medullary thyroid carcinoma RB1 Retinoblastoma 0 PCSK9 Hypercholesterolemia, autosomal dominant, 3 TSC1 Tuberous sclerosis 1 TNNT2 Left ventricular noncompaction 6 TSC2 Tuberous sclerosis 2 TP53 Li-Fraumeni syndrome 1 VHL Von Hippel-Lindau syndrome TGFBR1 Loeys-Dietz syndrome type 1A WT1 Wilms' tumor 16

17 Clinical Sample Submission Guidelines for Constitutional Testing General guidelines for constitutional testing: Specimen containers MUST be labeled with two unique identifiers (name and date of birth/medical record number). In general, extracted nucleic acids are only accepted from CLIA certified laboratories. Exceptions may be made at the discretion of the clinical laboratory director for specimens from research laboratories on a caseby-case basis. Informed consent is required for all clinical genetic testing performed at NYGC. Testing will not begin until the laboratory receives a completed, signed consent form. Specimen Type peripheral blood purified DNA saliva Amount Requested 2-5ml (call the laboratory before sending less than 2ml) 5μg (min. concentration of 50ng/μl A 260 /A ) 2mL (OrageneDx collection kit) Whole Exome Sequencing Container Type EDTA (lavender top) microcentrifuge tube (screw cap preferred) saliva collection tube (provided in OrageneDx collection kit ) Shipping Instructions Draw 2-5ml and invert tube 6-10 times to activate the anticoagulant. Ship immediately after collection (if possible) or refrigerate until ready to ship. Avoid extreme temperatures and do not freeze. Ship within 72 hours of collection. Ship overnight at ambient temperature in an insulated container. Use a cold pack during summer months. Ship overnight at ambient temperature in an insulated container. Use a cold pack during summer months. If using a kit other than the Qiagen QIAamp DNA blood mini kit, include a description or copy of reference material for the extraction kit used. Only genomic DNA is accepted. The laboratory does not accept products of amplification reactions. Follow the instructions prior to saliva collection. Ensure saliva sample tube caps are tightly secure. Saliva container must be placed inside the provided plastic bag, and then placed inside the biohazard bag. The saliva sample is stable at a wide range of temperatures once it is mixed with the DNA stabilization buffer liquid. Avoid extreme temperatures and do not freeze. Ship within 72 hours of collection. Ship overnight at ambient temperature in an insulated container. Use a cold pack during summer months. Ship specimens to: New York Genome Center Clinical Laboratory 101 Avenue of the Americas New York, NY