Types of Genome Sequencing Procedures

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 would otherwise be hidden until symptoms appeared. Whole genome sequence data can identify the following types of genomic alteration (those that involve large number of nucleotides are referred to as structural variants):

  • Single nucleotide variants (alterations that affect only one nucleotide at a time, also termed single nucleotide polymorphisms or SNPs)
  • Insertions and deletions (which can vary in size) in the DNA
  • Copy number variants (frequency of repetition of a particular DNA segment)
  • Translocations (rearrangements of genes or entire chromosome segments)

 

The client will determine what type of genome sequencing is appropriate for the subject of the genome sequencing procedure. The type of genome sequencing selected will depend on whether the subject is asymptomatic (expected to be healthy) or has disease symptoms. The options selected can impact both the genome sequencing procedure and the data analysis. Merogenomics Inc. will help the client find a third party service provider that matches the desired criteria at the highest standard and technological accuracy available. The cost of a single test can range from below $2000 to several thousand dollars, depending on the technical demands of the test. The following options are provided.

 

Genome Sequencing Procedures for Individuals with Symptoms

Genome Sequencing for Cancer Profiling

An individual who has been diagnosed with cancer can consider undertaking molecular profiling of the cancer sample through genome sequencing if that option has not be exercised in his or her clinical care. Access to such information can help pinpoint biological pathways affected by the cancer which could help identify personalized treatment options.1, 2

The cancer sample can be analyzed by itself or, for results of higher accuracy, in tandem with a normal tissue sample for comparison. A blood sample is required for normal tissue genome sequencing. A physician is required for client sample acquisition, and to interpret the genome sequencing report.

The cancer sample analysis might not provide information of value if there are no known approved or investigational therapies associated with the molecular profile of the cancer, or if the information conflicts with a therapy selected by the healthcare provider.

Additional tests can provide a more detailed molecular profiling of the cancer sample. This can include transcriptome sequencing (sequencing of RNA transcripts found in cancer tissue as a product of genome expression; such transcripts act as templates for protein production) and/or proteomics (which determines the identity and quantity of proteins found in cancer cells; such proteins are the most common targets of cancer drugs). The presence or absence of proteins can help to determine the chemosensitivity or chemoresistance of the cancer or indicate what type of monoclonal antibody therapy or hormonal therapy could be effective. The combined data analysis is generated using computer algorithms that parse available scientific information. Integration of multiple test procedures can enhance the accuracy of data interpretation and the success of outcome prediction.3, 4

Individuals diagnosed with cancer are encouraged to consider the advantages of utilizing RNA transcriptome sequencing, which can provide:

1) Information about the state of disease that cannot be derived from genome sequencing; for example, abnormal RNA transcript fusion that could be a contributing factor to cancer development

2) Validation of somatic variants (spontaneous mutations that were not inherited from parents) discovered in the cancer tissue genome

Merogenomics Inc. can also assist clients to investigate diagnostic options such as the use of cancer specific gene panels in addition to the whole genome sequencing procedure. Cancer targeted gene panels are tests that investigate only preselected genes. The whole genome sequencing procedure involves analysis of the entire genome in the cancer sample, providing a broader survey than the gene panels.

Information based on cancer sample molecular profiling is for education only. Integration of these data into a personalized therapy plan is determined by a healthcare provider or oncologist. 

Individuals who consider undergoing cancer genome sequencing should familiarize themselves with the limitations and risks associated with the procedure.

  1. Tsimberidou AM, et al. 2014. Personalized medicine for patients with advanced cancer in the phase I program at MD Anderson: validation and landmark analyses. Clin Cancer Res 20(18): 4827-36
  2. Uzilov AV, et al. 2016. Development and clinical application of an integrative genomic approach to personalized cancer therapy. Genome Med 8(1): 62
  3. Kim D, et al. 2015. Predicting censored survival data based on the interactions between meta-dimensional omics data in breast cancer. J Biomed Inform 56: 220-8
  4. Vazquez AI, et al. 2016. Increased Proportion of Variance Explained and Prediction Accuracy of Survival of Breast Cancer Patients with Use of Whole-Genome Multiomic Profiles. Genetics 203(3): 1425-38

 

Genome Sequencing for Disease Diagnosis

Persons with undiagnosed diseasesAn individual who suffers from a disease for which the cause has not been diagnosed can seek a genomic cause of the condition with a demonstrated success rate of up to 40%. Merogenomics Inc. will connect the client with a medical service where the subject’s genetic information will be analysed under the supervision of a clinical geneticist and a dedicated bioinformatician. The procedure requires personal trait information from, and a medical history of, the affected individual. Additional family members might need to have their genomes sequenced for comparative purposes. To ensure the highest level of accuracy, a blood sample will be required for DNA isolation to determine the genome sequence. The procedure involved in tracking the genetic cause of a disease requires more resources and involves higher financial input than does a straightforward genomic sequencing procedure.

The client will receive a digital copy of the entire DNA sequence in the subject’s genome, and an Analysis Report based on data derived from the genome sequence (please see below for details). Additional family members who have had their genomes sequenced will receive results independently. The medical team overseeing the genome sequencing procedure will have access to the produced genome DNA sequence and its interpretation.

If the diagnostic quest is successful, the supervisory medical team will suggest options of future steps (if any) that the client could undertake to deal with the newly categorized condition.

Genome Sequencing Procedures for Asymptomatic Individuals 

Genome Sequencing for Pregnant Mother / Fetus

A pregnant woman who desires to obtain the genome sequence of her fetus using a noninvasive procedure can provide a sample of her blood which contains DNA sources of both mother and future offspring. Because only the mother’s blood is required, the procedure is absolutely safe for the fetus. Genomes of both mother and fetus will need to be sequenced to deliver the genome sequence of the fetus, therefore two Analysis Reports can be delivered, one for the mother, and one for the fetus (see below for details). The fetus data will include sex assessment, rhesus D status, and chromosomal aneuploidies and rearrangements (within the scope of technical capability). Separate analysis reports will be issued regarding the genome of the mother and the genome of the fetus.

Testing is typically available from 10 weeks of gestation. Prenatal genome sequencing should not be considered a standalone test, and the client should be familiar with the test limitations, including the chances of a false-positive result, a false-negative result, or no result. However, one study based on nearly 150 000 pregnancy tests indicated a sensitivity of 99.17%, 98.24%, and 100% for trisomies 21, 18, and 13, respectively (a trisomy refers to the presence of three chromosomes, rather than the usual pair of chromosomes), and a specificity of 99.95%, 99.95%, and 99.96%, respectively.1 In a study of over 175 000 subjects, the sensitivity of chromosomal alterations ranged from 50–100%, depending on the size of the impacted genomic area and the depth of sequencing coverage.2

Pregnant women considering fetal genome sequencing should familiarize themselves with the limitations and risks associated with the procedure.

  1. Zhang H, et al. 2015. Non-invasive prenatal testing for trisomies 21, 18 and 13: clinical experience from 146,958 pregnancies. Ultrasound Obstet Gynecol 45(5): 530-8
  2. Helgeson J, et al. 2015. Clinical outcome of subchromosomal events detected by whole-genome noninvasive prenatal testing. Prenat Diagn 35(10): 999-1004

Genome Sequencing for Individual Screening

Any individual can choose to undergo a genome sequencing procedure to obtain information of value, including health related information for potential future care. The list of potential benefits is provided below. A client seeking such information about themselves (or a dependent) must provide a sample of saliva or blood. A blood sample is preferred because blood provides higher quality data than saliva. Saliva samples can contain bacterial contamination which can impact the accuracy of the genome sequencing.

What Client Obtains

The client will receive a digital copy of entire DNA sequence the subject’s genome (available for download via a secure website portal) and a customizable Analysis Report based on the latest scientific interpretation of the DNA sequence data, stratified from the most to the least clinically validated. The whole genome sequence will provide the following information.

Predisposition to disease development

This information lists the types of DNA alterations that have previously been associated with disease development. This includes the 56 genes published by the American College of Medical Genetics and Genomics as the minimum standard for patient notification.1 The largest suggested list of genes with clinical implications contained 2016 genes, including 161 actionable genes (medical intervention is available).2 It is highly recommended that the discovery of pathogenic or potentially pathogenic variants be verified with a secondary technology, as such mutations could lead to a disease state in either children or adults. The gene variants listed are based on the latest scientific interpretation of the DNA sequence data, and are stratified from the most to the least clinically validated in terms of their contribution to disease development. Proper interpretation of such results will require the oversight of a genetic counselor and/or appropriately trained healthcare provider. Although variants whose significance is currently unknown are not included in the list, future discoveries could link such variants to specific traits.

The information in this section is further subcategorized based on chosen client preferences (pathogenic actionable and nonactionable as well as adult-onset information).

  1. Green RC, et al. 2013. ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. Genet Med 15(7): 565-74
  2. Berg JS, et al. 2013. An informatics approach to analyzing the incidentalome. Genet Med 15(1): 36-44

 

Carrier status of conditions that might impact an offspring

Variants that we inherit from our parents can be either homozygous (identical variant copies were inherited from mother and father) or heterozygous (nonidentical variant copies were inherited from mother and father). Many inherited diseases are exhibited only if they are inherited in a homozygous state, that is, a deleterious variant was obtained from each parent. A heterozygous combination of variants might have no obvious clinical manifestation, whereas a homozygous combination of variants might lead to disease. Therefore, a healthy individual can be a carrier of a variant that can lead to disease in future generations. Current estimates suggest that 0.5–1% of the random couples will be carriers of same disease variants.1 Such couples have a 25% risk of having an affected offspring (that is, a one in four chance because each parent also carries a nondeleterious variant). Foreknowledge of carrier status can impact reproduction decisions.

  1. Gambin T, et al. 2015. Secondary findings and carrier test frequencies in a large multiethnic sample. Genome Med 7(1): 54

 

Pharmacogenomic information

Pharmacogenomics is a study of the correlation between the variations observed in the DNA sequence of an individual and the reaction of that individual to treatment with a drug; that is, whether the effect of the drug is adverse or efficacious. The pharmacogenomics science attempts to tailor a drug to fit an individual patient based on the patient’s genome information. Furthermore, the optimal drug dose can be chosen to match the individual metabolism phenotype, while avoiding adverse effects associated with toxicity or lack of efficacy. This is in contrast to the “one size fits all” approach that is currently used, even though it is known that drugs do not work the same way for everyone. Therefore genetic differences known to affect response to medications can be used to predict drug effectiveness for a specific individual.

Information related to health, such as predisposition to obesity

Genetic variants that are not associated with disease development can still be informative toward important health related trends. Variants associated with aging and longevity, insulin sensitivity, nutrient absorption, metabolic rate, etc., might indirectly impact the health of an individual.

Additional trait information

This information includes nonclinical traits such as hair loss, color blindness, and taste perception which have been scientifically linked to specific variants.

Ancestral information

People with similar ethnic backgrounds are more likely to share similar genetic variation. By mapping the pattern of inheritance among different groups of people around the world, ancestry relationships can be established. When a person has his or her genome sequenced, the pattern of shared DNA can point to the person’s ancestral origin. Such insights could have health related implications, as different ethnic groups are carriers of different health impacting variants.

The Analysis Report is for educational and research purposes only; it does not constitute a medical assessment, and it is not a substitute for professional medical advice, diagnosis, or treatment. The information presented in the Analysis Report cannot be used for medical or clinical purpose unless first interpreted by a licensed healthcare professional. A client who receives an Analysis Report that contains results with medical potential can book an appointment with a genetic counselor to answer health related questions.

Client Information Options

The sensitivity level (ranging from benign to pathogenic) of the genomic information presented in the Analytical Report will be graded according to the client’s request. The levels of concern regarding the identification of variants that clients can choose are listed below.

Pathogenic but nonactionable (untreatable) conditions [e.g., Huntington disease, spinal muscular atrophy]

A pathogenic variant is a mutation with direct consequences to human health. A pathogenic variant is considered “nonactionable” if the condition resulting from the pathogenic mutation is untreatable. Knowledge of nonactionable pathogenic variants can prepare the subject of genome sequencing for a possible condition, but such foreknowledge can involve significant psychological and social challenges. Therefore, a client must carefully consider whether the receipt of nonactionable pathological information is warranted. For example, only 5–25 % of individuals at-risk of Huntington disease development chose to take a confirmatory genetic test.1, 2 The likelihood of such incidental findings (~ 1–5% for all pathogenic variants)3-5 and the fact that the discovery of a pathogenic variant does not guarantee disease development also need to be considered.

  1. Creighton S, et al. 2003. Predictive, pre-natal and diagnostic genetic testing for Huntington's disease: the experience in Canada from 1987 to 2000. Clin Genet 63(6): 462-75
  2. Laccone F, et al. 1999. DNA analysis of Huntington's disease: five years of experience in Germany, Austria, and Switzerland. Neurology 53(4): 801-6
  3. Dorschner MO, et al. 2013. Actionable, pathogenic incidental findings in 1,000 participants' exomes. Am J Hum Genet 93(4): 631-40
  4. Gambin T, et al. 2015. Secondary findings and carrier test frequencies in a large multiethnic sample. Genome Med 7(1): 54
  5. Olfson E, et al. 2015. Identification of Medically Actionable Secondary Findings in the 1000 Genomes. PLoS One 10(9): e0135193

 

Pathogenic and actionable (treatable) conditions [e.g., cystic fibrosis, phenylketonuria]

“Actionable” incidental findings are mutations that are either pathogenic or likely to be pathogenic where intervention can be undertaken. This includes the 56 genes published by the American College of Medical Genetics and Genomics as the minimum standard for patient notification.1 However, Merogenomics Inc.’s recommendations will depend on the most up to date information presented in available public databases.

  1. Green RC, et al. 2013. ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. Genet Med 15(7): 565-74

 

Pharmacogenomic information [e.g., warfarin dosing]

Information regarding the impact of medication can be obtained from the DNA sequence in the whole genome. Specific mutations in the genome can suggest how an individual might respond to a specific medication, a field known as pharmacogenomics. In fact, 98% of surveyed U.S. physicians expect that patient genetic profiles, if available, would influence drug therapy. Many medical centers have begun to use personal genomic information to guide prescription choice. Treatment costs are thus reduced through enhanced monitoring of drug efficacy and toxicity.

Carrier status for recessive conditions [e.g., thalassemia]

Variants that we inherit from our parents can be either homozygous (identical variant copies were inherited from mother and father) or heterozygous (nonidentical variant copies were inherited from mother and father). Many inherited diseases are exhibited only if they are inherited in a homozygous state, that is, a deleterious variant was obtained from each parent. A heterozygous combination of variants might have no obvious clinical manifestation, whereas a homozygous combination of variants might lead to disease. Therefore, a healthy individual can be a carrier of a variant that can lead to disease in future generations. Current estimates suggest that 0.5–1% of the random couples will be carriers of same disease variants.1 Such couples have a 25% risk of having an affected offspring (that is, a one in four chance because each parent also carries a nondeleterious variant). Foreknowledge of carrier status can impact reproduction decisions.

  1. Gambin T, et al. 2015. Secondary findings and carrier test frequencies in a large multiethnic sample. Genome Med 7(1): 54

 

Adult onset conditions [e.g., breast cancer]

This item can include information for actionable and nonactionable pathogenic variants. Selection of this item can be omitted if there are ethical concerns in the case of a genome sequence being determined for a child.

There is a considerable ethical debate in the scientific community about the need to and right to inform minors of genetic indications that could impact their future health (i.e., conditions that are adult onset) as obtained from genomic sequencing. The stance taken by the American College of Medical Genetics and Genomics (ACMG) is that no age limitation should be set on the return of incidental findings that suggest a future health risk, as such results are likely to have important implications for other family members.1 However the ACMG acknowledges that, due to the novelty of human genome sequencing, there is a lack of available data “about the actual harms of learning about adult-onset conditions in children,” and such psychological impacts need to be taken into consideration when considering the use of such services.1 

Others argue that disease might never materialize, therefore a child should have a right not to be given information that could negatively impact his or her quality of life.2 The Canadian College of Medical Geneticists’ guidelines state that adult-onset genetic conditions should not be communicated unless disclosure could prevent serious harm to the health of other family members, and unless such disclosure is desired by the parents.3

  1. Green RC, et al. 2013. ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. Genet Med 15(7): 565-74
  2. Dickens BM 2014. Ethical and legal aspects of noninvasive prenatal genetic diagnosis. Int J Gynaecol Obstet 124(2): 181-4
  3. Zawati MH, et al. 2014. Reporting results from whole-genome and whole-exome sequencing in clinical practice: a proposal for Canada? J Med Genet 51(1): 68-70

 

Risk of multifactorial common diseases conditions [e.g., diabetes]

Common diseases such as heart disease and diabetes are polygenic in nature; that is, they comprise hundreds and even thousands of DNA variants whose interplay toward disease development is unclear.

Such variants can explain about 10% of the genetic component of the disease at best, even if the impact of all associated variants is combined, and therefore they have low predictive value.1-4 As these variants currently have either no clinical validity or unclear validity, testing for them is not typically offered in a clinical setting.5

This information can be presented to the client for future reference while recognizing the limitations of such information.

  1. Meigs JB, et al. 2008. Genotype score in addition to common risk factors for prediction of type 2 diabetes. N Engl J Med 359(21): 2208-19
  2. Paynter NP, et al. 2010. Association between a literature-based genetic risk score and cardiovascular events in women. JAMA 303(7): 631-7
  3. Richards S, et al. 2015. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med 17(5): 405-24
  4. Voight BF, et al. 2010. Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. Nat Genet 42(7): 579-89
  5. Weaver M and Pollin TI 2012. Direct-to-Consumer genetic testing: what are we talking about? J Genet Couns 21(3): 361-6

 

Nonmedically related traits and information [e.g., ancestry, hair loss]

Nonmedical information can also be obtained, such as heritage background, nonhealth related trait information, or information with indirect medical impact, such as a predisposition to obesity.

Potential personal psychological consequences for the client or the immediate family should be considered, and each client is encouraged to seek genetic counseling prior to the genome sequencing procedure.

Personal information, whether collected from the client or generated through genome sequencing, will be kept private and confidential. All data and information will be encrypted, password protected, and stored in a cloud. Merogenomics Inc. will not distribute private and sensitive information to third parties without the agreement of the client. Third party access to a client's genome will be solely for the purpose of data generation and/or analysis.

A Merogenomics Inc. representative is available to answer questions you may have regarding the procedure.

 

 Additional Products

  • genomic counseling
  • pathogenic variants verification
  • digital biobank storage