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Full genome sequencing for undiagnosed

Full genome sequencing for undiagnosed

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A full genome sequencing DNA test assesses all of the DNA within the genome of an affected patient towards the diagnosis of a disease that cannot be obtained by other standard medical means.

In order to obtain the DNA testing kit under medical supervision (required), the purchased test includes a bill to be presented at your selected clinic. Test prices can vary between different medical clinics. PATHOGENIC RESULTS WILL REQUIRE A GENETIC COUNSELING SESSION PRIOR TO MEDICAL MANAGEMENT.

Clients will also be given a checklist of topics to facilitate informed consent. Test purchase should take place after consultation with a Merogenomics representative in order for the client to be best prepared for informed consent. Informed consent and education towards its understanding will be required by the clinic. IF YOU HAVE NOT CONSULTED MEROGENOMICS ABOUT YOUR DNA TEST PLEASE BOOK A FREE APPOINTMENT USING THE LINK BELOW PRIOR TO TEST PURCHASE!

All international or Canadian clients in a region without a supported medical clinic, please book a meeting with Merogenomics to discuss the use of your preferred local doctor.

Human genome sequencing is the process of decoding the order of nucleotide bases in the entire human DNA to gain information of interest. Variations observed in the DNA between different individuals afford insight into the variation in specific traits of these individuals. As some traits have an impact on human health, genome sequencing can provide valuable information about human disease that is currently unobtainable or very challenging to obtain by other standard medical means. Test prices can vary between different medical clinics. Volume discounts available.

 

  • Whole genome sequencing (including nuclear and mitochondrial DNA), provides the most comprehensive view of alterations in an individual’s DNA code
  • This test is used for clinical purposes and should not be regarded as investigational or for research
  • The test must be ordered by a medical doctor who will overview the clinical report based on the DNA sequence interpretation
  • The test is for persons with a suspected genetic and undiagnosed condition and is used when an unclear condition cannot readily be linked to a clinical diagnosis due to:
    • The failure of prior testing to identify a genetic explanation
    • No other testing being available for the presented conditions
    • The clinical presentation cannot be matched to a known genetic disorder
    • Multiple genes may be responsible for the condition
  • The purpose of the test is to determine if a genetic diagnosis can be uncovered, leading to a condition diagnosis and potential medical management changes
  • Suspected conditions compatible with full genome sequencing include:
    • Brain malformations
    • Congenital heart defects and cardiomyopathies
    • Epilepsy disorders
    • Mitochondrial disorders
    • Movement disorders
    • Neurodegenerative and neurodevelopmental disorders
    • Neuromuscular disorders
    • Neuropathies
    • Ophthalmology and hearing loss disorders
    • Skeletal disorders
    • Sex development disorders
  • This test is not for individuals interested in proactively screening themselves for health predispositions and drug responses. Please  refer to the "Full genome sequencing" section for a screening test for otherwise presumed healthy individuals
  • Anonymized patient/client clinically-relevant information will be included in public databases to help with the future medical analysis of human genomes. Databases contain cumulative results from around the world and do not include information that can personally identify the patient/client
  • This test only provides diagnosis results relevant to the condition attempting to be diagnosed. The test does not provide secondary findings or pharmacogenomic findings unless further requested by the ordering physician. This test does not provide information on traits that are not medically relevant, such as eye color, fitness performance, and tasting. The test does not analyze ancestry. The patient/client will always have the option of analyzing their DNA for any additional purposes by an independent third-party. Merogenomics recommends checking the quality of any company prior to submitting the DNA for such additional analysis, and confirming whether there is scientific validity behind the information being investigated
  • The test might not provide a diagnosis if either the causes of the condition are not genetic in nature, or the causative variant is not identified. Even with a successful DNA diagnosis, it is possible that the information might not help in predicting a prognosis or change medical management or the treatment of the disease
  • The test can be paid for directly by the patient/client. Interest-free payment plans are available. Insurance billing is available and can be investigated up-front to determine out-of-pocket expenses. A patient assistance program is available for patients meeting income criteria. Institutional billing is also available for organizations that prefer to bill patients/clients directly

  • Merogenomics provides background education towards patient/client informed consent
  • The collection kit can be for a saliva or a blood sample, with prepaid shipping included
  • Services are fully insured, and are HIPAA, CLIA and CAP compliant
  • The test will provide the DNA code of nearly the entire genome using the current best sequencing systems, stored on cloud for the patient/client by the company
  • The results are available within 12 weeks
  • A concise clinical report signed by a medical geneticist is delivered to the ordering doctor only, and then subsequently discussed and shared with the patient/client
  • The report will include primary findings that are directly related to the cause of the disease for the patient. No further analysis of the genome is done
  • Secondary findings unrelated to the medical condition but which might impact the patient’s health can be reported for the patient if requested. It includes findings in a set of 73 genes as recommended by the American College of Medical Geneticists (ACMG) for incidental findings. This is a list of genes that are linked to different disease developments for which intervention or disease treatment options are available
  • Pharmacogenomic information could be applied if the disease area is provided with a list of drugs
  • The decoding and interpretation of the genome is done utilizing industry gold-standard tools and databases, which also include proprietary systems developed in-house – one of the key determining factors of test quality for medical use
  • Board-certified medical geneticists will work with the ordering physician to provide a collaborative diagnosis, so that doctors can be as involved in the process as desired
  • The ordering doctor will obtain their own personal login to the diagnostic web console in order to have direct access to all of the data, including any preliminary findings requiring immediate attention
  • Previous medical information of the patient/client already collected by  the ordering physician will be incorporated into the analysis
  • Follow-up management will be suggested based on the patient’s diagnosis and available medical history
  • The genome sequence can be re-analyzed in the future using in-silico panels of selected genes (based on the list of suspected phenotypes/diseases), to obtain additional diagnoses if new symptoms appear in the patient. This allows for the incorporation of novel patient medical information and the latest scientific interpretation
  • If the diagnosis is not made, the company will periodically re-analyze the genome data (based on a pre-defined schedule or clinical databases update), and automatically alert the doctor if relevant new findings arise
  • If the diagnosis is not made, sequencing of additional family members can be considered to aid in the identification of the DNA change leading to the medical condition. Such comparisons of genomic data between family members can make the diagnosis easier, although patient genome sequencing alone is usually enough. Please see the section titled “Additional Options” for cost information
  • The genome sequence can be provided to the patient/client upon request using a secure FTP server download
  • Testing is usually done with children with up to a 50% success rate

  • To obtain a diagnosis when other standard testing methods fail to provide a clear answer. A diagnosis is made for DNA variants considered strong causal candidates for a genetic disorder, variants associated with increased disease risks, or variants involved in drug dosing and/or drug toxicity for certain medications. Studies show that the sequencing approach often leads to a diagnosis more quickly and with lower overall costs than other methods.
  • The diagnosis can provide the possibility of guiding or influencing medical care management as follows:
    • Treatment of the already existing condition
    • One can potentially be released from unnecessary clinical surveillance, including potentially invasive diagnostic procedures
    • Intervention to prevent worsening of the condition from developing
    • Preparation for the outcomes, whether through education or by seeking clinical trials
  • The diagnosis might influence the considerations of additional family members regarding testing, or affect reproductive decisions to avoid passing the same DNA alterations to future offspring
  • Only a single whole genome sequencing test is required for an individual. The complete sequence information captured in the test allows for an unlimited number of future data reanalysis as more scientific evidence is uncovered, or as new health symptoms materialize, so it provides the best ROI for the investment made. Whole genome sequencing captures small sequence changes, structural variants, tandem repeat expansions and mitochondrial variants, both in the coding and non-coding regions, all in a single test
  • Patient/client data is securely stored on cloud for subsequent re-analysis. Data is never sold, or shared with any third-parties unless specifically requested by patient/client. Such data sharing will require a separate consent form to be signed by the patient/client in addition to the one that is signed to obtain the test
  • The entire process closely follows the Canadian and American guidelines, therefore there is a high level of proper accountability for the clinic

  • The “entire genome sequence” refers to the current feasibility of technology, as an entire genome is actually not decoded because no single technology exists to be able to sequence the full human reference genome. The current employed technology generates data that typically includes over 98.5% of the known human genome
  • Biological sample quality can influence the scope and quality of the final decoded DNA sequence data, and therefore its interpretation
  • It is never possible to guarantee that every DNA change in the genome will be found, therefore a negative result cannot rule out the possibility that the patient carries an unexamined mutation
  • Certain alterations or variants might not be identified due to the presence of highly homologous pseudogenes (the presence of inactive genes that are highly similar in sequence to active genes), or other confounding factors such as bone marrow transplantation, blood transfusion, or mosaicism (the presence of different variants in a subset of cells in an individual)
  • The limitations of the sequencing technology might not allow for the complete uncovering of large structural changes within the genome, and might require additional technologies in order to be achieved. Genome sequencing typically focuses on the small sequence alterations and might have a limited scope in the analysis of the gross alterations (such as a segment of a chromosome inverting or moving to a new location)
  • False positive results can occur and all clinically relevant identified alterations are recommended to be validated by separate technology
  • The average genome read depth is 30X, but such read depth cannot cover the entire genome. Each patient will present their own unique read depth distribution across the genome. About 0.5% of the genome will be sequenced with a read depth of less than 8X, which is the minimum that is considered high enough to make a statistically confident call about the observed DNA sequence
  • The test does not detect alterations which are not caused by a change in the DNA sequence, such as gene expression, epigenetic modifications, fusion, chromosome conformational changes, or X-linked recessive mutations in females who manifest disease due to skewed X-inactivation
  • The interpretation will be limited to the current state of scientific knowledge of how DNA changes lead to a disease. This scientific knowledge can also contain mistakes
  • Samples cannot be accepted if the patient/client has undergone an allogenic transplant such as bone marrow or a peripheral stem cell transplant. A history of hematological disease might exclude test availability in certain circumstances. Contact Merogenomics to discuss potential alternatives
  • Psychological consequences can be severe with high risk individuals and patients/clients should be screened prior to testing
  • The test does not consider somatic alterations (non-inherited DNA changes acquired post-birth throughout one’s lifetime)
  • The test has not been cleared or approved by the US Food and Drug Administration. The FDA does not require this test to go through a premarket FDA review

  • All tests offered through Merogenomics require a physician to sign a test requisition form for regulatory compliance reasons. Once the requisition form is signed by the doctor, the ordering doctor does not have to participate in the process until the receipt of the test results
  • Merogenomics can provide detailed background information to the ordering physician on the test process. Merogenomics also provides additional education towards patient/client informed consent
  • The test is for persons with a suspected genetic and undiagnosed condition, and is used when an unclear condition cannot readily be linked to a clinical diagnosis. The purpose of the test is to determine if a genetic diagnosis can be uncovered, leading to a condition diagnosis and potential medical management changes. For individuals interested in proactively screening themselves for health predispositions and drug responses, please  refer to the “Population Screening for Disease Risk” section
  • Suspected conditions compatible with full genome sequencing include:
    • Brain malformations
    • Congenital heart defects and cardiomyopathies
    • Epilepsy disorders
    • Mitochondrial disorders
    • Movement disorders
    • Neurodegenerative and neurodevelopmental disorders
    • Neuromuscular disorders
    • Neuropathies
    • Ophthalmology and hearing loss disorders
    • Skeletal disorders
    • Sex development disorders
  • It is recommended by sequencing guidelines that the patient/client undergoes genetic counseling prior to and after clinical DNA testing
  • The DNA sequencing takes place in a CLIA/CAP certified laboratory with subsequent DNA data interpretation performed in an additional CLIA certified laboratory. The interpretation of the DNA data is based on public and private databases of clinical past observations. The final results are overseen and signed by a board-certified medical geneticist prior to delivery to the doctor. This provides one of the highest levels of regulatory oversight towards the generation of clinically meaningful genomic results for patient medical management
  • Patient data is HIPAA compliant, securely stored on cloud for continuous re-analysis, and never sold or shared with third-party companies
  • The ordering physician will obtain access to the data with an easy-to-use web console during and post genome sequencing with all of the clinically relevant results. Merogenomics can offer an explanation of the web console use. Merogenomics will not have access to the patient/client data using the web console
  • Proprietary gene selection based on disease phenotypes (using HPO nomenclature), is used to help determine a diagnosis
  • The ordering physician will be the recipient of the genome sequencing analysis clinical report. The patient/client will not obtain these results independent of the ordering physician. The patient will likewise not gain access to the web-based portal or the final report. Therefore the ordering physician will be providing the information contained in the report to the patient/client. Merogenomics will not have access to the patient/client report, but can review the report after the receipt of the data if requested by the patient/client
  • The report is designed with doctors in mind and will be divided into the following sections:
    • The first page will have a condensed summary listing all of the clinically relevant results ordered into sections:
      • Pathogenic or likely pathogenic results – the information requiring the utmost attention spanning the entire genome
      • ACMG 73 status – the 73 genes tied to the clinical conditions that are the most strongly recommended by the American College of Medical Genetics and Genomics guidelines to be reported to patients if they are affected and should be requested to be analyzed
      • Other – mitochondrial or structural variants. Structural variants are alterations of the genome involving large segments of DNA
      • Follow-up recommendations
    • The second page will list details about each of the mutations and the corresponding condition
    • The final pages are devoted to the methods of testing and the limitations of the procedure
    • Pharmacogenetic results are provided in an independent report if requested by the ordering physician, and are provided only for the list of medications submitted for analysis. This information relates to drug response and/or toxicity based on public databases listing clinically valid results
  • The service provider’s board-certified medical geneticists can provide a second opinion concerning medical management
  • There is an automated periodic reanalysis of unsolved cases. The ordering physician is notified if any new findings related to the case arise
  • Samples cannot be accepted if the patient/client has undergone an allogenic transplant such as bone marrow or a peripheral stem cell transplant. A history of hematological disease might exclude test availability in certain circumstances
  • For cancer patients undergoing chemotherapy treatment, the DNA quality may be affected if the patient has received treatment in the past 120 days, potentially requiring sample resubmission

  • The DNA sample is prepared using TrueSeq PCR-Free Library and is sequenced using Illumina HiSeq X Ten System at 30X mean mappable coverage with an average of 5% of the genome covered at ≥20X, with 97.3% of the genome covered at ≥8x and 99.4% of HGMD and ClinVar annotated variants covered at ≥8x
  • The test offers95% sensitivity, 99.99955% specificity and 99.6% positive predictive value for SNVs. 97.9%, 96.0% and 95.2% sensitivity for indels of 1-5, 6-15 and 16-50 nucleotides respectively. 96% clinical sensitivity for structural variants
  • Extracted genomic DNA can also be submitted for sequencing, if it has been isolated from a CLIA-certified laboratory or equivalent
  • State of the art bioinformatics tools are used based on the Broad Institute’s gold-standard and best practices for alignment and variant calling
  • Extensive data quality control is utilized: mapped read percentage, percentage of properly paired reads versus failed reads and duplicate reads, coverage statistics, gender and pedigree concordance
  • Proprietary methods identify and analyze four types of variants:
    • Small sequence changes
      • Single nucleotide variants (SNVs, alterations that affect only one nucleotide at a time, also termed single nucleotide polymorphisms or SNPs)
      • Insertions and deletions (indels under 50 bp)
    • Structural variants (DNA alterations that affect large segments of DNA of more than 50 bp, and can include insertions, deletions, inversions, breakpoints or copy number variations or CNVs: the duplication of a particular DNA segment)
    • Trinucleotide repeat expansions (repetition of a small DNA segment)
    • Mitochondrial variants
  • Variants are classified as pathogenic, likely pathogenic, or of unknown significance according to the established guidelines by the American College of Medical Genetics and Genomics /Association for Molecular Pathology from 2015 (Richards S et al. 2015. Genet Med 17(5): 405–424)
  • Structural variants larger than 3 Mbp in size are reported. Smaller structural variants are reported only when pathogenic or are likely pathogenic and related to the patient/client’s phenotype
  • Mitochondrial DNA includes sequence variants and indels under 20 bp only. Heteroplasmy (the presence of more than one type of mitochondrial genome), is reported to the level of ≥4%
  • Clinically relevant short tandem repeat expansions are reported for >20 known pathogenic loci without identifying a specific repeat number
  • Best-in-class public and commercial databases and tools used for annotations:
    • Disease association: HGMD Professional, Genome Trax, ClinVar, OMIM, Orphanet, Gene Tests
    • Population frequencies: gnomAD, dbSNP, ensemble, 1000 Genomes Project, ExAC, NHLBI Exome Sequencing Project and service provider proprietary database
    • Severity prediction: SIFT, MutationAssessor, MutationTaster, GWAVA, PolyPhen2, FATHMM, LRT
    • Conservation prediction: SiPhy, GERP++, PhyloP, PhastCons
    • Gene essentiality: according to Georgi B et al. 2013. PLoS Genet 9(5):e1003484
    • Gene tolerance: RVIS score according to Petrovski S et al. 2013. PLoS Genet 9(8):e1003709
  • Customizable medico-legal documentation can be provided and include: electronic patient questionnaire, patient informed consent, physician disclaimer, research and clinical use documentation, and territory specific materials

  • Expedited results are available within 4 weeks for an additional cost
  • Family trio (two parents and an offspring), is a sequencing option available at $5,597 USD. An accurate assignment of family relationships is necessary for a successful analysis of the family trio full genome sequencing. The biological relationships between submitted family samples will be assessed to ensure that the parental relations were correctly identified. If a discrepancy is identified, the ordering physician will be notified and the sequencing of the parental samples will be cancelled
  • Access to a genetic counselor is available before and/or after the receipt of the test results for an additional cost. This is highly recommended, especially after the results are received
  • All pathogenic or likely pathogenic results can be verified by separate independent Sanger sequencing technology for an additional cost
  • The DNA sequence data is available for download by the paying client using a secure web portal at no extra cost. The file format is available either as FASTQ/BAM (the entire sequence data from the patient’s submitted sample), or as a VCF file (a list of variants that differ from the human genome reference that was used for the alignment of the client genome data)
  • Extracted genomic DNA can also be submitted for sequencing, when it is isolated from a CLIA-certified laboratory or equivalent. Contact Merogenomics to discuss additional alternatives
  • Volume discounts are available starting with a minimum of five samples. Contact Merogenomics for more details

Purchase of the test can be refunded within 30-days of issued invoice date minus $50 processing fee to cover the costs associated with testing kit (even if the kit was not used by the customer). A refund is not available once the sample has been obtained by the laboratory and DNA testing has commenced.

Dr. Denis Vincent Clinic

138-8627 91 St NW, Edmonton AB

Preventous Collaborative Health

1635 17 Ave SW, Calgary AB

Summerwood Medical Centre

162-4005 Clover Bar Rd, Sherwood Park AB

Please contact us if your clinic is interested in providing access to DNA testing.

Merogenomics is collaborating with a third party institution, Blue Finance, to provide access for eligible customers to convenient, monthly payment options. Contact Merogenomics for more information.

Below are examples of possible monthly payment options for specified duration terms.

 

Payment options for 12 month term

DNA test cost Monthly payment
$699 $65
$799 $85

 

Payment options for 24 month term

DNA test cost Monthly payment
$2,499 $127
$3,749 $190
$4,099 $208
$5,199 $264
$7,399 $376