Issue 12 | December 2017
Strand Genomics ezine issue 12

Welcome to Strand Genomics

Strand Life Sciences welcomes you to Strand Genomics, our monthly E-zine that includes articles of interest to physicians. 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. Please also feel free to write back to us with comments and questions at

Breast Cancer and Obesity: Adding More Risk Factors to the Mix in India

 Dr. Shefali Sabharanjak
Strand Life Sciences


  • Molecular mechanisms of obesity and metabolic syndrome may have a role to play in development of breast cancer.
  • Genes involved in insulin dysregulation, obesity-linked inflammation and signalling via adipokines can enhance the process of carcinogenesis in breast tissues.
  • Obesity is a rising trend in India and the Asian subcontinent which can act as a significant contributory factor towards incidence of breast cancer as well.
  • Anthropometric measurements such as truncal obesity and waist-to-hip ratios in pre- as well as post-menopausal women can be used to identify individuals at risk of breast cancer.


Breast cancer looms large over the healthcare scenario in India. Statistical estimates show that breast cancer has overtaken cervical cancer as the number 1 cancer in terms of incidence (Asthana et al. 2014). In the earlier issues of Strand Genomics, we have discussed other factors like the high incidence of germline mutations in the Indian population. The mortality rate of breast cancer is also high considering the fact that one out of every two breast cancer patients diagnosed in India is lost to the disease (; Section: Mortality Ratio of Breast Cancer).

In addition to a genetic predisposition towards breast cancer, socio-economic factors like lack of knowledge, lack of safe social milieux to discuss intimate health problems and inhibitions associated with openness about women’s health issues are also contributory factors (Khokhar 2013; Khokhar 2012). Although the contribution of heredity towards the overall epidemiology of breast cancer is high and is reflected in the trend towards greater incidence in young women (, there are predictive genetic tests designed to assess every person’s individual risk status. People who choose to undergo prophylactic risk assessment and germline testing can be encouraged to undergo regular medical surveillance and keep an eye on their health.


Figure 1. Factors Contributing to Rising Incidence of Breast Cancer in India


Factors Contributing to Rising Incidence of Breast Cancer in India

Obesity in Cahoots with Breast Cancer

High Blood Sugar and Insulin Like Growth Factors

An emerging factor that can heighten the risk for breast cancer in women is obesity. Truncal obesity, evident as expanding waistlines and increasing waist-to-hip ratios, can increase the risk for breast cancer in pre- as well as post-menopausal women (Nagrani et al. 2016). In addition to anthropometric measurements, recent research has helped to identify genes and SNP markers that are common to obesity and cancer.

Molecular mechanisms that are the hallmark of obesity are inflammation, insulin resistance and dysregulation of the adipokine system (Simone et al. 2016). Insulin resistance can develop from increased circulatory levels of insulin-like growth factors IGF-1 and IGF-2 as well as reduction in the expression of IGF-binding proteins IGFBP-1 and IGFBP-2. IGFBP-1 can inhibit the growth of xenografted human breast cancer cells, suggesting that physiological mechanisms like obesity, that suppress the expression of this protein, can indirectly promote the growth of breast cancer cells.

IGF-1 and estrogen can synergistically stimulate the RAS/MEK/MAPK/ERK1/2 (mitogen-activated protein kinase/extracellular signal-related kinase 1/2) and PI3K/AKT/mTOR (phoshatidylinositol-3 kinase/murine thymoma viral oncogene homolog/mammalian target of rapamycin) proliferative pathways (Motallebnezhad et al. 2016).

Another self-sustaining cycle of gene expression is the effect of serum glucose concentration on the WNT pathway. Genetic variants of the transcription factor TCFL7-2, which is involved in hepatic glucose regulation by the WNT pathway, are also associated with high risk for breast cancer as well as hyperglycaemia (Simone et al. 2016).

Genetic variants of IGF-1 have also been linked with increased risk of postmenopausal breast cancer, even accounting for modifiable risk factors like diet and exercise (Jung et al. 2017).


Activation of the transcription factor, NF-κB resulting in cell proliferation is also evident in inflammatory conditions.

Local as well as systemic inflammation characterized by markers such as TNF-α, IL-1β, IL-6 and others can lead to activation of NF-κB, thereby stimulating cell proliferation. Adipocytes can also release free fatty acids that can stimulate signalling via the Toll-like receptor -4 (TLR-4) pathway, ultimately activating proliferative activity of NF-κB (Balaban et al. 2017). Moreover, adipocyte cell death is marked by the presence of macrophages with crown-like structures, a feature that is evident in cancerous breast tissues as well.

Adipokine Status

Hormones such as leptin and adiponectin play an important role in the regulation of metabolism of fat cells. Additionally, leptin can activate signalling via the APK/ERK1-2, PI3K/AKT/mTOR, Janus kinase 2/signal transducer and activator of transcription 3 (JAK2/STAT3) pathway, culminating in the activation of NF-κB in breast tissues.

Leptin-mediated signalling events can also trigger the non-canonical pathways that include PKC, JNK and p38 MAP kinase (Guo et al. 2012).

NF-κB activates transcription of proliferative and anti-apoptotic factors such as CCND1, c-MYC, JUN, FOS, and BCL2, thereby promoting growth of breast cancer cells.

Perhaps the most pronounced effect of adipokines is the effect of adiponectin on the nuclear availability of BRCA1. Adiponectin is a positive effector of the peroxisome proliferator activated receptor-γ (PPAR-γ) pathway, which in turn, activates mechanisms that control cell growth. Low levels of adiponectin can lead to deficient stimulation of the PPAR-γ pathway. This results in reduction in nuclear translocation of the BRCA1 protein (Simone et al. 2016). Given the role of BRCA1 in DNA repair mechanisms, insufficiency of BRCA1 can lead to carcinogenesis in breast tissues.

Obesity: An Upward Trend

Increasing urbanization, adoption of sedentary lifestyles and dietary changes are culminating in an obesity epidemic, worldwide. A recent assessment of global trends in obesity has clearly marked an acceleration in the rates of obesity in children and adolescents in Asian countries (Abarca-Gómez et al. 2017). Incremental trends in obesity have been noted amongst urban Indian women as well (Gouda & Prusty 2014), with increasing economic affluence. The linkage between obesity and breast cancer clearly enhances the risk of breast cancer in Indian women.


  • Molecular mechanisms of obesity and metabolic syndrome may have a role to play in development of breast cancer.
  • Genes involved in insulin dysregulation, obesity-linked inflammation and signalling via adipokines can enhance the process of carcinogenesis in breast tissues.
  • Obesity is a rising trend in India and the Asian subcontinent which can act as a significant contributory factor towards incidence of breast cancer as well.
  • Anthropometric measurements such as truncal obesity and waist-to-hip ratios in pre- as well as post-menopausal women can be used to identify individuals at risk of breast cancer.


Abarca-Gómez, L. et al., 2017. Worldwide trends in body-mass index, underweight, overweight, and obesity from 1975 to 2016: a pooled analysis of 2416 population-based measurement studies in 128·9 million children, adolescents, and adults. The Lancet, 390(10113), pp.2627–2642. Available at: [Accessed December 20, 2017].

Asthana, S. et al., 2014. Breast and cervical cancer risk in India: an update. Indian Journal of Public Health, 58(1), p.5. Available at: [Accessed December 14, 2016].

Balaban, S. et al., 2017. Adipocyte lipolysis links obesity to breast cancer growth: adipocyte-derived fatty acids drive breast cancer cell proliferation and migration. Cancer & metabolism, 5, p.1. Available at: [Accessed December 20, 2017].

Gouda, J. & Prusty, R.K., 2014. Overweight and obesity among women by economic stratum in urban India. Journal of health, population, and nutrition, 32(1), pp.79–88. Available at: [Accessed December 20, 2017].

Guo, S. et al., 2012. Oncogenic role and therapeutic target of leptin signaling in breast cancer and cancer stem cells. Biochimica et Biophysica Acta (BBA) – Reviews on Cancer, 1825(2), pp.207–222. Available at: [Accessed December 20, 2017].

Jung, S.Y. et al., 2017. Interaction of insulin-like growth factor-I and insulin resistance-related genetic variants with lifestyle factors on postmenopausal breast cancer risk. Breast Cancer Research and Treatment, 164(2), pp.475–495. Available at: [Accessed December 20, 2017].

Khokhar, A., 2012. Breast cancer in India: where do we stand and where do we go? Asian Pacific journal of cancer prevention: APJCP, 13(10), pp.4861–6. Available at: [Accessed October 11, 2017].

Khokhar, A., 2013. View point: How to make women familiar with their breasts? Asian Pacific journal of cancer prevention: APJCP, 14(9), pp.5539–42. Available at: [Accessed October 11, 2017].

Motallebnezhad, M. et al., 2016. The insulin-like growth factor-I receptor (IGF-IR) in breast cancer: biology and treatment strategies. Tumor Biology, 37(9), pp.11711–11721. Available at: [Accessed December 20, 2017].

Nagrani, R. et al., 2016. Central obesity increases risk of breast cancer irrespective of menopausal and hormonal receptor status in women of South Asian Ethnicity. European Journal of Cancer, 66, pp.153–161. Available at: [Accessed August 18, 2017].

Simone, V. et al., 2016. Obesity and Breast Cancer: Molecular Interconnections and Potential Clinical Applications. The oncologist, 21(4), pp.404–17. Available at: [Accessed December 19, 2017].

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Under-Utilisation of Genetic Tests in Triple Negative Breast Cancer

Triple negative breast cancer

Triple negative breast cancer (TNBC) is highly prevalent amongst Indian breast cancer patients. About 31% of Indian breast cancer patients are diagnosed with TNBC.

Internationally accepted guidelines for genetic testing state that all TNBC cases should be referred for genetic testing to understand if hereditary mutations can be identified. Naturally, if TNBC patients are found to be carriers of BRCA1 or BRCA2 mutations, then their eligibility for PARP inhibitor therapy to achieve synthetic lethality with chemotherapy gets established. Findings from one of recent surveys however point to a gap between the incidence of TNBC and inclusion of germline genetic analysis in therapeutic regimens. About 27.7% of physicians with more than 50% patients younger than 50 years of age, indicated that genetic testing was not advised for TNBC in their practice. Likewise, 22.9% physicians with less than 50% of their patients younger than 50 years of age had TNBC patients that were not advised genetic testing. Considering the rising trend towards younger age of diagnosis of breast cancer amongst Indian women, germline tests can provide better therapeutic options to such patients.

ctDNA-guided Change of Therapy Improves Quality of Life of a Lung Cancer Patient

–  Dr. Shefali Sabharanjak
Strand Life Sciences


  • Tripti Vasudev*, aged 61 years, was diagnosed with NSCLC.
  • Genetic analysis revealed the presence of an EGFR mutation – EGFRL858R at the initiation of therapy.
  • The patient was prescribed Afatinib as a first-line therapy. However, lung cancer persisted and the patient was advised to undergo a rebiopsy as well as the Strand Liquid Biopsy Test (Strand Advantage Sense & Resist Tests) to understand the overall tumor heterogeneity.
  • High systemic tumor burden, with a distinct bias towards the EGFRT790M mutation, was noted in the analysis of ctDNA by liquid biopsy.
  • The patient was switched to Osimertinib therapy and further progression of the patient is being monitored using periodic liquid biopsies.
  • An accurate assessment of overall tumor load as well as tumor clonality is provided by a combination of liquid and solid biopsies.
  • Concurrent evaluation of solid tumor tissue as well as liquid biopsy led to comprehensive evaluation of a patient, leading to better therapeutic choices. Genetic analysis of the second lung cancer biopsy ALONE would have supported the continuation of Afatinib therapy, eventually leading to failure of therapy.


Lung cancer has the distinction of being the cancer with the fastest fatality. In most cases, the overall survival of lung cancer patients is no longer than 9-12 months post-diagnosis (Murali et al. 2017). In India, the prevalence to incidence ratio of lung cancer is the lowest amongst all solid tumors.


Table 1. Prevalence / Incidence Ratio for Lung Cancer is the lowest in India (Takiar & Jayant 2013)


Breast 5
Cervix 5
Ovary 3
Stomach 1
Lung 1
Mouth 4

Considering the rapid loss of health of lung cancer patients, prognostic aids that can help to assess the status of a patient during therapy would be of tremendous value. Although imaging techniques like PET-CT are available, newer technologies like liquid biopsy to obtain a sample of tumor DNA (known as ctDNA) can be used very effectively to assess patient status (Marmarelis et al. 2017; Vendrell et al. 2017; Hou et al. 2017).

Patient Profile

Tripti Vasudev, a retired accountant aged 61 years, had moved from Patna to Bhubaneshwar in 2015. She was glad to escape the pollution of Patna and looked forward to a healthy and quiet retirement. Despite relocating to a cleaner environment, she noticed that her persistent low cough had not gone away. In fact, her breathing difficulties had increased slowly but steadily. She consulted a renowned doctor in Bhubaneshwar who advised her to undergo a CT-scan to understand the root cause of her problems. Small areas of abnormal growth (nodules) were evident in the CT-images and hence Tripti was advised to undergo a lung biopsy to withdraw a sample of the tissue.

Histopathological investigations confirmed that Tripti had developed Non-Small Cell Lung Cancer (NSCLC), type adenocarcinoma. A full–body scan revealed the presence of similar nodules all over the body as well.

Treatment Options

Tripti was advised treatment with Afatinib, a targeted therapy molecule. This drug inhibits the activity of the EGFR protein, which is mutated in most adenocarcinoma cases. However, her oncologist noted that the tumor persisted and response to afatinib therapy waned, a few months into the therapy. A fresh biopsy of the lung tumor was advised to understand the genetic profile of the persistent NSCLC, in a second attempt. The StrandAdvantage 48-Gene Tissue Specific Test (Lung) was prescribed for identification of mutant genes as well as other molecular markers.

Tripti’s oncologist also advised her to take advantage of novel liquid biopsy tests which can facilitate tracking of the tumor via a blood sample, at any point of time, during the therapy.

Results of Genetic Testing

The StrandAdvantage 48-gene test, a pan-cancer test was prescribed for Ms. Tripti Vasudev, in the second biopsy of her lung cancer. This test is designed to identify mutations in genes that are mutated in most solid tumors.

Table 2. Genetic Analysis of the Second Lung Biopsy- Solid Tissue Sample

identify mutations in genes


Tripti’s lung cancer tissue showed two mutations in the EGFR gene, namely EGFRL858R and EGFRT790M. Tumors bearing these mutations can be effectively targeted with drugs like Afatinib and Osimertinib, respectively. Afatinib therapy had already been administered to her, during the preceding months.In order to assess the tumor burden present in other organ systems as well, a liquid biopsy test for detection of tumor DNA in the blood was also performed.

A Liquid Biopsy for cancer is a novel ‘Blood Test’ for cancer. Cancer cells, like normal cells, shed DNA into the blood as a part of regular tissue turnover. This DNA is known as ‘cell-free DNA’ (cfDNA). It is possible to extract cfDNA from blood and then check for the presence of DNA released by cancer cells. DNA derived from cancer cells is called ‘circulating tumor DNA’ (ctDNA). The amount of ctDNA present in the blood is a good indicator of the total tumor burden, present in a patient.

Analysis of ctDNA from the Liquid Biopsy

Table 3. EGFRSense and Resist Tests- Tumor heterogeneity Identified by Liquid Biopsy

Analysis of ctDNA from the Liquid Biopsy


The EGFR mutations identified in the solid tumor sample were also detected in the liquid biopsy sample that had been taken from the patient at the same time. Moreover, the number of copies of ctDNA present per ml of plasma indicated that the tumor burden in Tripti is very high. In fact, Tripti is one of the rare patients who are able to survive despite having such a high tumor load.

Since Tripti had been undergoing Afatinib therapy, the prevalence of the EGFRL858R mutation was lower than that of the EGFRT790M mutation. These results indicated that her lung cancer was changing its genetic profile and cells with the EGFRT790M mutation were becoming more dominant than cells which respond to Afatinib treatment.

Comparison with Lung Biopsy

The prevalence of the same mutations in the second lung tissue biopsy was also assessed.

Table 4. Prevalence of EGFR Mutations in the Second Solid Lung Biopsy

Solid Tumor Result


Genetic analysis of the solid tumor (second lung biopsy sample) shows that the EGFRL858R mutation is the more prevalent one compared to the EGFRT790M mutation.
However, since the cancer is metastatic, the overall tumor burden and the predominant tumor genotype present in the rest of the body were assessed with greater accuracy via the liquid biopsy test.

Figure 1. Comprehensive Assessment of Cancer Status by Simultaneous Genetic Analyses of Solid & Liquid Biopsies


Change in Therapeutic Regimen

The evolution of lung cancer from Afatinib sensitivity to resistance has been documented in several studies. Emergence of the EGFRT790M mutation is one of the mechanisms that can make lung cancer resistant to Afatinib therapy (Xiong et al. 2017; Facchinetti et al. 2017).

Considering the high prevalence of the EGFRT790M mutation in the liquid biopsy result, Afatinib therapy was terminated for Tripti in August 2017. Instead, she is now undergoing therapy with Osimertinib – a drug that is designed to target cells with the EGFRT790M mutation. As of November 2017, Tripti is responding well to the new treatment.

Monitoring Progression

Tracking the progression of possible resistance to Osimertinib as well as development of other genomic rearrangements is now possible using subsequent Liquid Biopsy tests.


  • In Tripti’s case, the prognostic technique that provided greater insight into her overall tumor load was the assessment of ctDNA in the liquid biopsy sample.
  • Genetic analysis of the second lung cancer biopsy ALONE would have supported the continuation of Afatinib therapy, eventually leading to failure of therapy.
  • An accurate assessment of overall tumor burden as well as the emerging dominance of the EGFRT790M mutation was provided by liquid biopsy based detection and quantification of ctDNA.
  • Liquid biopsy tests can be performed, at physicians’ discretion, without the encumbrance of radioactive tracers and specialized imaging equipment.
  • Rapid change of therapy from one targeted therapy drug to the next appropriate one has improved the quality of life of the patient and provided further options for therapy. The combination of genetic analysis of the solid tumor and the liquid biopsy sample proved to be highly advantageous to the patient. If the liquid biopsy test had been overlooked, Tripti would have continued to receive ONLY Afatinib treatment with the result that Afatinib –resistant lung cancer cells would have continued to grow in her body. Massive metastasis would have increased her risk for fatality. Instead, the liquid biopsy results proved to be a warning, just in time. The comprehensive genetic profile of the tumor, in the lungs as well as from all over the body, was the deciding factor in the choice of another targeted therapy drug that increased her quality of life.

*- Patient names changed to protect privacy


Facchinetti, F. et al., 2017. Mechanisms of Resistance to Target Therapies in Non-small Cell Lung Cancer. In Handbook of experimental pharmacology. Available at: [Accessed November 28, 2017].

Hou, H. et al., 2017. Discovery of targetable genetic alterations in advanced non-small cell lung cancer using a next-generation sequencing-based circulating tumor DNA assay. Scientific reports, 7(1), p.14605. Available at: [Accessed November 21, 2017].

Marmarelis, M. et al., 2017. Emerging uses of circulating tumor DNA in advanced stage non-small cell lung cancer. Annals of translational medicine, 5(18), p.380. Available at: [Accessed November 22, 2017].

Murali, A.N. et al., 2017. Outcomes in Lung Cancer: 9-Year Experience From a Tertiary Cancer Center in India. Journal of Global Oncology, 3(5), pp.459–468. Available at: [Accessed November 27, 2017].

Takiar, R. & Jayant, K., 2013. A model approach to calculate cancer prevalence from 5 year survival data for selected cancer sites in India. Asian Pacific journal of cancer prevention: APJCP, 14(11), pp.6899–903. Available at: [Accessed November 20, 2017].

Vendrell, J. et al., 2017. Circulating Cell Free Tumor DNA Detection as a Routine Tool forLung Cancer Patient Management. International Journal of Molecular Sciences, 18(2), p.264. Available at: [Accessed March 13, 2017].

Xiong, L. et al., 2017. Dynamics of EGFR mutations in plasma recapitulates the clinical response to EGFR-TKIs in NSCLC patients. Oncotarget, 8(38), pp.63846–63856. Available at: [Accessed November 28, 2017].

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Advanced genomic analysis for answers not found before

Clinical Trials Update

breast cancer

Palbociclib In Combination With Letrozole As Treatment Of Post-Menopausal Women With HR+ HER2- Advanced Breast Cancer




Clinical Study Identifier: NCT02679755

Sponsor: Pfizer

Currently, a clinical trial testing the efficacy of palbociclib along with letrozole for treatment of ER+ve /PR+ve and HER2-ve breast cancer is underway, in Bangalore.

Patients with the following profile are eligible for this study:

  • Post-menopausal women (>=18 years of age) with proven diagnosis of advanced carcinoma of the breast (ER(+) and/or PgR(+) and HER2(-)) who are appropriate for letrozole therapy (in the first-line advanced/metastatic disease setting).
  • Eastern Cooperative Oncology Group (ECOG) performance status 0-2.
  • Adequate bone marrow, liver, and renal function.

Patients with prior therapy with CDK inhibitors as well as patients with high risk of cardiovascular disease including long QT syndrome and Torsade de pointe are not eligible for this study. The trial is being conducted at Manipal and HCG hospitals in Bangalore, India.

More information about the trial:

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