Issue 16 | April 2018
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Welcome to Strand Genomics

Strand welcomes you to Strand Genomics, our monthly E-zine that includes articles of interest to physicians like you. We have a new version of this e-zine!! Strand Genomics brings the latest news in the world of genetic diagnostics, to your doorstep. We present carefully crafted articles as well as curated news in the field of cancer therapy and genetic analyses to support the implementation of personalized medical care. We invite you to peruse as well as share these articles. A new feature is the section that provides updates on clinical trials in India as well as on recently-approved drugs for cancer. Now that Strand and Triesta Sciences have joined hands to create a synergistic, end-to-end diagnostic services company, ask our sales representatives about all the tests we can provide for your specialty! Feel free to write back to us with comments and questions at strandlive@strandls.com.

Timely Interventions Enabled by Liquid Biopsy

Dr. Shefali Sabharanjak
Strand Life Sciences

Abstract

  • Timely and periodic snapshots of cancer are the need of the hour in delivering personalized cancer therapy.
  • Genetic profile determination can help to estimate tumor load as well as clonal heterogeneity of cancers especially of those that are suspected to be metastatic.
  • The program is designed to deliver personalized treatment of cancer patients, based on periodic and accurate judgment of residual disease.
  • A simple blood sample is enough to provide a qualitative and quantitative genetic profile of cancer.
  • Elimination of dependence on sophisticated technology mandatory for image-based diagnostics is instrumental in making it cost-effective for patients.

Introduction

Cancer therapy has two major hurdles:

  1. Identifying the right therapy to maximize a patient’s quality of life without trial-and-error.
  2. Gaining deeper insights into a patient’s status throughout therapy.

Cancer is not a uniform disease. Although meta-classifications based on the tissue of origin hold true, like tumors derived from lung tissue can all be understood as lung cancers, there exist finer distinctions within these, that can be best understood in terms of the genetic profiles of the tumors. The genetic barcode of each patient’s tumor- essentially the genes that are mutated- in that particular patient is an important differentiator. The genetic profile of a tumor can serve as an identifier as well as a determinant of therapy choices. Genetic profiles can be determined by NGS analyses of solid tumor tissue preserved in formalin-fixed paraffin (FFPE) blocks as well as from periodically drawn blood samples (liquid biopsies) from cancer patients.

Leveraging Information from Genetic Profiles

Genetic testing for somatic cancers is gaining acceptability in clinical practice. However, in India, social constraints such as cost and patient awareness are major hurdles in the implementation of genetic testing. Most genetic tests are leveraged at a point when traditional chemotherapy has been ineffective at halting the growth as well as metastasis of somatic cancers. Given that clonal evolution of tumors is a distinct possibility in the metastatic stage, obtaining a comprehensive genetic profile of all tumor clones, becomes vital. A single genetic test, even with optimal timing might not be adequate to provide the most accurate and latest profile of cancer in a patient.

In the post-surgical period, a liquid biopsy can be performed, before the initiation of adjuvant chemo-/ radio-therapy. The timing of this test can be adjusted as per the monitoring oncologists’ discretion. Comparison of the genetic profile of the solid tumor as well as the tumor load evident by circulating tumor DNA (ctDNA) assessments in the first liquid biopsy, is expected to provide an almost real-time picture of the patient’s status. Any differences evident in the genetic profile can indicate development of cancer sub-clones. Similarity between the readouts of the liquid biopsy and the original tumor will indicate the presence of residual disease. Moreover, ctDNA measurements are quantitative and are also positively correlated with patient prognosis. Higher levels of ctDNA indicate greater tumor load and possibly poor prognosis (Delfau-Larue et al., 2018). Therefore, an accurate estimation of tumor load and clonality will enable oncologists to choose as well as time adjuvant chemotherapy for the best patient outcomes.

In the event that adjuvant chemotherapy is initiated, the additional liquid biopsy steps can be executed at suitable time intervals, taking into consideration the patient’s response as per other clinical indicators as well. These tests can be easily interspersed with other radio-imaging tests, thereby reducing radiation exposure, while still providing a snapshot of cancer.

Cost Mitigation

A recent study has indicated that medical surveillance of patients is cost-effective only for colorectal surgery patients but not for breast cancer patients (Barbieri, Richardson, & Paisley, 2018). Medical surveillance using mammograms or other imaging techniques is a resource-intensive strategy. Liquid biopsies, can be used in the time period between two image-based tests in order to monitor the patient as well as gain insights into the residual disease with quite minimal effort. A trained phlebotomist can draw a simple blood sample that can yield adequate amounts of cell-free (cfDNA) and ctDNA.

Strand CancerMAP

Strand CancerMAP is designed to meet precisely these challenges in cancer therapy. This program is a personalized assessment of the status of cancer, with tests included to provide periodic snapshots of cancer.

Strand Cancer MAP - Product OverviewStrand Cancer MAP- MAP stands for My Awareness Program- is best suited for patients who are eligible for surgical tumor removal. The program includes:

  1. NGS analysis of solid tumor sample obtained from surgery
  2. A liquid biopsy test that can be performed BEFORE adjuvant chemotherapy
  3. Two liquid biopsy tests to be performed during the course of the adjuvant chemotherapy

The NGS analysis of the surgicised tumor can yield the genetic profile of the primary tumor. This effective baseline measurement can help to understand whether specific targeted therapies are likely to be effective against residual tumor cells or not. This decision alone is expected to make a significant difference to the quality of life of the patient.
The StrandCancerMAP program is expected to yield significant benefits in cases of breast, ovarian, lung and colorectal cancer. The program also features other patient support mechanisms such as regular alerts about upcoming tests and a personalized counsellor to guide the patient at each step. The Strand CancerMAP program can therefore be a useful ally in the war against cancer.

Summary

  • Timely and periodic snapshots of cancer are the need of the hour in delivering personalized cancer therapy.
  • Genetic profile estimation can help to estimate tumor load as well as clonal heterogeneity of cancers especially of those that are suspected to be metastatic.
  • The Strand CancerMAP program offers a powerful combination of genetic analysis of solid tumors as well as strategically timed liquid biopsies.
  • The program is designed to deliver personalized treatment of cancer patients, based on periodic and accurate judgment of residual disease.
  • The CancerMAP program is cost-effective owing to the inclusion of liquid biopsies for monitoring cancer, at the oncologists’ discretion.
  • A simple blood sample is enough to provide a qualitative and quantitative genetic profile of cancer.
  • Elimination of dependence on sophisticated technology mandatory for image-based diagnostics is instrumental in making it cost-effective for patients.

References

Barbieri, M., Richardson, G., & Paisley, S. (2018). The cost-effectiveness of follow-up strategies after cancer treatment: a systematic literature review. British Medical Bulletin. http://doi.org/10.1093/bmb/ldy011

Delfau-Larue, M.-H., van der Gucht, A., Dupuis, J., Jais, J.-P., Nel, I., Beldi-Ferchiou, A., … Itti, E. (2018). Total metabolic tumor volume, circulating tumor cells, cell-free DNA: distinct prognostic value in follicular lymphoma. Blood Advances, 2(7), 807–816. http://doi.org/10.1182/bloodadvances.2017015164

 

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Watch “Diagnosis of Rare Diseases using NGS-based Multi-gene Testing – Case Studies” a webinar presented by Dr. Aparna Ganapathy

Watch this recorded webinar on multi-gene NGS-based genetic testing for rare diseases

A disease is considered to be ‘rare’ when it affects one in about 2000 individuals in the population. While each disease individually might be rare, collectively, the overall incidence could be very high in a particular population or country causing a significant socio-economic burden. Arriving at a confirmatory diagnosis is a major challenge in these inherited disorders, yet can significantly impact treatment and disease management. Conventional genetic testing for rare diseases focuses mostly on sequencing of fewer genes, followed by a deletion/duplication analysis by multiplex ligation-dependent probe amplification (MLPA). This sequential testing strategy is time consuming and very expensive. Multi-gene panel tests based on NGS (next-generation sequencing) enable detection of all types of mutations, including large deletions/ duplications, thus providing comprehensive genetic testing in a cost-effective manner. With the advent of NGS technology, the possibility of offering a ‘single platform solution’ for all types of genetic defects has become a reality.

This webinar highlights some of our interesting case studies wherein multi-gene testing with NGS was helpful in arriving at a confirmatory as well as differential diagnosis, even for complex clinical conditions. With robust bioinformatic analysis, we were able to detect several complex variations which a conventional test had missed.Watch now

Germline Cancer Testing in A Proband: Extension of Benefits to Unaffected Family
Members

Dr. Shefali Sabharanjak
Strand Life Sciences

Abstract

  • The Strand Germline Cancer Test helped identify a likely pathogenic mutation in the MLH1 gene of 52-year-old Sohanlal Shah*.
  • The test result coupled with a detailed family history confirmed the incidence of Lynch syndrome in the family.
  • Mutation-specific test was offered to Mr. Shah’s family members and used by 7 relatives.
  • 5 family members tested negative, 2 tested positive but were unaffected by cancer at the time of testing.
  • The advance warning of the presence of a genetic mutation that increased their risk of developing cancer allowed them to adopt surveillance measures in order to catch any future incidence of cancer as early as possible.

Introduction

Most cancers are caused by genetic damage resulting from random mutations and exposure to cancer-causing substances. However, a small percentage of cancers are caused by inherited mutations that are passed on from generation-to-generation.

Typically, individuals who have a defective cancer-causing gene, are prone to suffer from cancer at an early age, and are also likely to have primary cancers in one or more organs, eg breast and colon. Incidence of cancer at a young age poses significant financial and socioeconomic challenges.

Hereditary Breast and Ovarian Cancer (HBOC) syndrome, Peutz-Jeghers syndrome, Lynch syndrome, Cowden syndrome are some examples of hereditary cancer syndromes. Genetic tests are available to understand the mutation status of 19 genes that are associated with some of the well-known hereditary cancer syndromes. The unique utility of this test (called the Germline Cancer Test) is that it can be used for people with a confirmed incidence of cancer to understand whether their cancer is familial or sporadic cancer.

Additionally, the test can be used by normal (unaffected) individuals in a pre-emptive mode, in order to understand their personal risk for developing cancers. Risk management strategies can be brought into practice to identify symptoms of cancer in the early stages.

Patient Profile

Sohanlal Shah*, aged 52 years, had a thriving spice trade in Ahmedabad. He had a busy work life, but physical activity coupled with a sensible vegetarian diet helped him maintain a healthy lifestyle.

His family members had been diagnosed with various kinds of cancers, and sometimes he wondered whether more bad news was in store for him. When he started having symptoms of pain during bowel movements and frequent episodes of diarrhea, he consulted his primary care physician. In turn his physician directed him to consult Dr. Shirish Alurkar, a renowned oncologist in Ahmedabad.

Family History

Clinical investigations revealed that Sohanlal was suffering from colorectal cancer. A preliminary enquiry into the incidence of cancers in Sohanlal’s family suggested that the family may be carrying a hereditary mutation. Hence, Dr. Alurkar suggested a counselling session with a genetic counselor from Strand, in order to understand the family history in detail.

A genetic counselor is trained to understand inheritance patterns of genes and suggest the choice of a Germline or a Somatic test for genetic analysis. A pedigree chart was constructed to capture the incidence of cancer in Sohanlal’s family.

Family Tree Pre-Genetic Testing

 

Family Tree Pre-Genetic Testing

Figure 1. Family tree of Sohanlal Shah

Sohanlal has 3 sisters and a brother. One of his sisters, Smriti, had been diagnosed with endometrial cancer at the age of 39 years. Their mother, Maniben, had been diagnosed with colorectal cancer when she was 65 years old and had succumbed to the disease. Her sister (Maala, Sohanlal’s maternal aunt) had lost her life to endometrial cancer at the age of 60 years.

Sohanlal has three maternal uncles and all had been diagnosed with colorectal cancer at 40 years (Dipesh), 50 years (Darshan), and 50+ years (Suresh) of age, respectively. Darshan, who succumbed to colorectal cancer, had two sons and a daughter and both the sons, Jayesh and Nilesh had been diagnosed with colorectal cancer, at the ages of 50 and 39 years, respectively.

Sohanlal’s cousin, Umedbhai (Suresh’s son) had been diagnosed with duodenal cancer at the age of 35 years. Another cousin, Jignesh was also battling colorectal cancer. All in all, 7 family members were battling cancer at the time of Sohanlal’s diagnosis.

Going even further into the earlier generation, Sohanlal’s grandfather Jivajibhai had lost his life to colorectal cancer at the age of 70 years.

Given the high prevalence of colon cancer as well as endometrial cancer in the family, a diagnosis of ‘hereditary non-polyposis colorectal cancer’ was suspected. The Strand Germline Cancer Test was prescribed to Sohanlal to understand if hereditary mutations were present in his genome.

Results of Genetic Testing

A ‘likely pathogenic’ variant of the MLH1 gene – a deletion in exon 2 – was identified in Sohanlal’s genome. Sohanlal is heterozygous (carries one copy) for this mutation. However, since mutations in MLH1 are inherited in an autosomal dominant manner, one mutant copy is sufficient to cause colorectal cancer (Kohlmann & Gruber, 1993).
Key Findings of Genetic Test for suspected Lynch Syndrome patient

  • A mutation in exon 2 of the MLH1 gene was identified in Sohanlal’s genome.
  • The identified heterozygous deletion (c.156delA) will cause a frameshift leading to premature termination of the protein (p.Glu53ArgfsTer4).
  • The truncated protein is predicted to have a length of 56 amino acids (aa) as opposed to the original length of 756 aa. As a result, the truncated protein is likely to lack the functionally important ATPase domain, the MutS interaction domain as well as the PMS2/MLH3/PMS1 interaction domain of the MLH1 protein, which will likely cause loss-of-function.
  • The identified variant is in the vicinity of several other variants that are known to be associated with Lynch Syndrome. Hence, the variant has been classified as a ‘Likely Pathogenic’ variant.
  • The proband was advised about the chances of passing on this mutation to his son, Sahil. In addition, mutation-specific testing was offered to the immediate relatives of the proband to understand their status.

Mutation-Specific Testing

A mutation-specific test (MST) is a test designed to assess the presence or absence of specific mutations within a proband’s genome. This test was offered to other family members, Parthiv, Chaarvi, Sahil, Amod and Preeti, in 2015, in order to determine whether they had inherited the same mutation or not. Sohanlal’s siblings, Parthiv, Chaarvi and Preeti were negative for the MLH1 mutation. Sohanlal’s son, Sahil, and nephew Amod were positive for the MLH1 mutation and were unaffected by cancer at the time of testing.

In 2017, Suyash and Neha (Parthiv’s children) wanted to understand their personal risk for cancer, despite the fact that their father was negative for the tested mutation, and took the same MST as their cousins.

Sohanlal Shah's family tree after genetic testing

Surveillance Measures against Cancer

A positive identification of a pathogenic or likely pathogenic germline mutation in a person’s DNA can be used as a preparatory signal for increased surveillance against cancer. Sahil and Amod were unaffected by cancer at the time of testing. They were advised about their risks for developing various types of cancers and were provided with the following guidelines by NCCN, to take care of their health (see Table 1). Adoption of these surveillance measures can help to spot the signs of cancer at the very earliest, thereby increasing their chances of having many therapeutic options, including surgical removal in the early stages.

Table 2. Health Surveillance Advice for Carriers of MLH1 Germline Mutations
surveillance options for carriers of <em>MLH1</em> mutations

Conclusions

  • Sohanlal, a 52-year-old man from Ahmedabad was diagnosed with colorectal cancer and was advised genetic testing.
  • Sohanlal’s family history indicated a strong likelihood of hereditary non-polyposis colorectal cancer (Lynch Syndrome) in the family.
  • The Strand Germline Cancer Test facilitated the identification of an MLH1 mutation in the patient’s DNA.
  • The mutation is in the vicinity of other known pathogenic mutations in the MLH1 gene. Considering the location and the predicted effect on the produced protein, this mutation was classified as a ‘likely pathogenic’ one.
  • Mutation-specific testing of seven other family members led to the identification of two members who have inherited the same pathogenic mutation but were unaffected at the time of testing. Five other relatives of the proband have tested negative for this germline mutation.
  • The proband’s son and nephew who are heterozygous carriers of this germline mutation have been advised to adopt surveillance measures to spot the earliest signs of cancer.
  • Germline cancer tests can be leveraged for pre-emptive care and to actually reduce one’s personal risk for cancer considerably.

*- Patient names changed to protect privacy

References

Kohlmann, W., & Gruber, S. B. (1993). Lynch Syndrome. GeneReviews®. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/20301390

Download this case study in PDF format.

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Advanced genomic analysis for answers not found before

Clinical Trials Update

Peri-operative Trastuzumab study for patients with operable breast cancer

Clinical Study Identifier: CTRI/2013/12/004263

Sponsor: Roche

A Phase III Double Blind Randomized Placebo Controlled study of Trastuzumab as Short Duration Preoperative Therapy in patients with HER2-neu Positive Operable Breast Cancer

Patients with the following profile are eligible for this study:

  • Age: 18-65 years
  • Gender: Female
  • Confirmed breast cancer patients

Patients with any of the following conditions are excluded from this study:

  • Bilateral breast cancer
  • Active uncontrolled cardiac disease, including cardiomyopathy,
    CHF (New York Heart Association [NYHA] functional classification of 3 or 4), unstable angina, and myocardial infarction (within 12 months of study entry).
  • Inadequately controlled hypertension (ie, systolic blood pressure [BP] > 180 mm Hg or diastolic BP > 100 mm Hg).
  • Family history of congenital long or short QT syndrome, Brugada
    syndrome or QT/QTc interval > 0.45 second or known history of
    QT/QTc prolongation or torsade de pointe (TdP).
  • Significant chronic gastrointestinal disorder with diarrhea as a major symptom.
  • Women who are pregnant or breast-feeding.

The trial is being conducted at Tata Memorial Center Mumbai, India.

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