CC BY
5УДК 616.006.6:615.37 DOI: 10.37279/2224-6444-2021-11-2-115-122
GENOMIC SCIENCE-BASED PERSONALIZED TREATMENT FOR CANCER
Varghese Jeffy Vianneys1, Sorokina L. E.2, Rebik A. A.2, Regan O. V.2
'Department of General and Clinical Pathophysiology, 2Central Research Laboratory, Medical Academy named after S. I. Georgievsky of V. I. Vernadsky Crimean Federal University (Medical Academy named after S.I. Georgievsky of Vernadsky CFU), 295051, 5/7, Lenin Avenue, Simferopol, Russia
For correspondence: Sorokina L.E., Central Research Laboratory of Medical Academy named after S.I. Georgievsky of Vernadsky CFU, e-mail: leya.sorokina@mail.ru
Для корреспонденции: Сорокина Л. Е., Центральная научно-исследовательская лаборатория, Медицинская академия им. С.И. Георгиевского ФГАОУ ВО «КФУ им. В.И. Вернадского», e-mail: leya.sorokina@mail.ru
Information about authors:
Varghese Jeffy Vianneys, http://orcid.org/0000-0002-2197-8230 Sorokina L. E., http://orcid.org/0000-0002-1862-6816 Rebik A. A., https://orcid.org/0000-0001-5346-3998 Regan O. V., https://orcid.org/0000-0001-9839-0761
SUMMARY
At present, cancer is a rising dreadful issue all around the world, as it is among one of the main leading causes for mortality globally. Recent improvements in genetic engineering called genome sequencing provides a different approach in the treatment of cancer. Genome sequencing is a technique used for determining the complete composition of the DNA sequence of a genome. The cancer genomic project and the cancer genome atlas are initiatives taken by different countries to analyze and store the genomic sequence variations of different tumor cells from a diverse population. Sequencing malignant cells have pointed the unique abnormalities like mutations in the genes, which shows the exact cause for the uncontrolled cell division in many types of malignancies. We discuss the recent effective method called next-generation sequencing which has the ability to sequence DNA molecules in thousands, simultaneously, rapidly, and cost- effectively. NGS can detect all types of mutations and chromosomal abnormalities. This information provides a detailed and improved understanding of different types and subtypes of cancer from their molecular basis. The process includes sequencing of both tumor and normal genome from the same individual, and then are examined and verified. This data is used to provide a personalized treatment routine for that specific patient which can improve their prognosis. The various challenges and limitations of NGS which are hindering the advancement and the probability of using it in clinical oncology are also discussed which include ethical problems and abundant data generated causing an issue in data analysis. We outline the recent promising developments in implementing genomic science in the personal and targeted treatment of cancer for better prognosis and plausible cure for malignancy in the near future.
Key words: genome sequencing; cancer; personalized treatment; next-generation sequencing.
ПЕРСОНАЛИЗИРОВАННАЯ ТЕРАПИЯ РАКА -ДОСТИЖЕНИЯ ГЕНЕТИЧЕСКОЙ МЕДИЦИНЫ
Варгхесе Джеффи Вианнейс1, Сорокина Л. Е.2, Ребик А. А.2, Реган О. В.2
'Кафедра общей и клинической патофизиологии, ^Центральная научно-исследовательская лаборатория, Медицинская академия им. С. И. Георгиевского ФГАОУ ВО «Крымский федеральный университет им. В. И. Вернадского», Симферополь, Россия
РЕЗЮМЕ
В настоящее время злокачественные новообразования являются одной из основных причин смертности во всем мире, причем в последние годы наблюдается тенденция к росту заболеваемости, что представляет собой серьезную проблему. Современные достижения генной инженерии, такие как секвенирование генома, обеспечивают инновационный подход к лечению рака и представляют значительный практический и научный интерес. Секвенирование - метод, используемый для определения полного состава последовательности ДНК генома. Проекты «Cancer genomic project» и «Cancer genome atlas» - инициативы, предпринятые странами для анализа и хранения вариаций геномных последовательностей различных опухолевых клеток из разных популяций. Секвенирование злокачественных клеток выявило уникальные аномалии, которые позволили установить точную причину неконтролируемого деления клеток при многих типах злокачественных новообразований. В статье обсуждается современный эффективный диагностический метод, называемый секвенированием следующего поколения (next-generation sequencing - NGS), который позволяет упорядочивать тысячи молекул ДНК одновременно, выполнять анализ быстро и экономично. NGS может обнаруживать все типы мутаций и хромосомных аномалий, а эта информация обеспечивает подробное и улучшенное понимание патогенеза различных типов и подтипов рака на их молекулярной основе. NGS включает в себя секвенирование как опухолевого, так и нормального генома пациента, а затем анализ и сопоставление полученных данных. Результаты используются для составления персонализированного плана лечения конкретного пациента, который может улучшить прогноз. В статье представлены недавние многообещающие разработки в области применения NGS в таргетной терапии рака, обеспечивающие лучший прогноз при злокачественных новообразований.
Ключевые слова: секвенирование генома; рак; персонализированаая таргетная терапия; секвенирование нового поколения.
2021, т. 11, № 2
Cancer is always considered to be a disease without a satisfactory prognosis due to the various peculiarities among different types and also individually. The GLOBOCAN 2020's report on the incidence of 36 types of cancer in 185 countries worldwide, estimated 19.3 million new cases of cancer. The international agency for research on cancer, produced a report on the mortality due to cancer globally in 2020 with almost 10 million deaths due to the mentioned [1].
It is also established that the new cases of cancer are most likely to increases in the upcoming decades mainly due to new mutations, smoking, and an unhealthy diet.
The major developed countries seem to be having high rates of new cancer cases like prostate and breast cancer in men and women respectively and lung cancer plays an important part in increasing the mortality rate. An observatory study in the United States of America concluded the transition from cardiovascular diseases to cancer as the leading cause of death in 41% of countries in 2015, which increased from 21% of countries in 2003 [2]. This shift from heart pathology to cancer is increased mostly in high-income countries.
The major complication of type 2 diabetes leading to death mostly directs to cardiovascular complications and stroke, but the following research says different. The Ayrshire Diabetes follow-up cohort study conducted a population-based study among the Scottish type-2 diabetes patients to determine the primary reason for their mortality between the years 2009 and 2014. The results illustrated cancer, accounting for almost 27.8% of it, making cancer the most common cause of mortality, then only followed by heart diseases at 24.1% [3].
A recent study estimated a significant increase in cancer incidence among adolescents and young adults, and also that it would increase in the upcoming years according to its survey [4].
Proper understanding of any specific cancer about its exact etiology and pathogenesis will give a clear picture and a path for a better prognosis. It can be achieved by the technique called genome sequencing, which is the process involved in determining the entire DNA sequence of a genome. Particularly the recent most reliable platform under genome sequencing known as next-generation sequencing (NGS), which can even sequence in a day the entire genome of a human being [5]. It provides a promising platform in genetic engineering to produce specific personalized treatment regimen for the exact needs of cancer patients which will improve the prognosis and lead to a better life.
Genome sequencing
Genome is the part of DNA that contains the genetic information needed for survival, and
the whole genome sequencing goes through all the necessary sections of the person's genetic information. Whereas the exome is the part 0f the genome, exactly where the sections of genome contain instructions for protein synthesis.
Exome sequencing test is a more focused technique to find the genetic variations that cause the disease. Genome sequencing is used for many reasons, some of them being, diagnostics- to confirm whether the pathology is caused due to a genetic condition; predictive- to find the probability of chances to inherit a specific genetic disorder in a fetus with the disorder running in the family; carrier screening- to check for the presence of any mutations causing them to be a heterogenous carrier of a dominant disease, which may be a risk factor for passing the disorder to the child; or maybe just to find and understand the ancestry and common traits, mainly used in paternal or maternal identification. The variations found in the genome sequencing are the alterations in the DNA sequence which differ from the nucleotide sequence of most people, which may or may not indicate any previously discovered genetic disorder. But in most cases, the mutations or variations are unspecific and do not direct to a particular disorder, in this case, these data are stored in a common system which will have much information like this sort of data from different patients and they could be matched to find similar mutations or variations in the DNA sequence and lead to the accurate finding of a new genetic linked pathology.
Genetic variations even under a particular subtype of malignancy could be displayed in a vast variety of either point mutation, deletion, inversion, insertion or even translocation in different patients' presentation of the disease. Acute promyelocytic leukemia is proven in a study to be presented in different variety of mutations which has also been presented with a similar morphological presentation, clinical manifestations and course. In the study APL was seen to be associated with diverse PML-RARA splice variants, absurdly unusual translocations, insertions, multiple RARA fusion partners, and also a RARG fusion partner [6].
From the above study, it is quite evident that the same type of cancer could be presented and as well caused by a totally different genomic modification at the molecular level, even with the same or mostly similar clinical course and presentation of the disease among the diseased. This example is ample to require a call for more personalized therapy requirement, as treating different diseases having different etiology and genetic patterns the same drug will obviously not help much in the improvement of the disease. So, detailed analysis and understanding of the DNA variation will help to
conduct proper drug interaction clinical trials which specifically target the faulty gene. Evolution of Genome Sequencing DNA sequencing was first introduced around 1970 by Sanger and his team workers called as Sanger sequencing [7]. It could easily be called as a beginning of an era in the genetic field as this method paved the way for all the then future next- generation sequencing techniques which all overcome the various limitations of Sanger sequencing by being more time-saving and cost-effective than the previous versions. This old method of sequencing used Polyacrylamide Gel Electrophoresis (PAGE) radiographically to detect the terminated sequences. Since then the genome sequencing has evolved to a better stage by replacing many steps and techniques, some being radiographical sequence method been replaced with using separate fluorescence for different nucleotide. Next-Generation Sequencing Many different companies and laboratories around the world use different methods for sequencing. Here we review about one of the best technologies used by many researchers, doctors, and institutes worldwide, which is the Illumina. They use the technology which was developed by Solexa and Lynx Therapeutics in the beginning called as bridge amplification [8; 9].
RNA-Seq SNP-Seq Bisulfite-Seq
FAIRE-Seq MAINE-Seq chjp ^
Figure 1. Comparison between Sanger sequencing and next-generation sequencing (NGS) technologies. Sanger sequencing is limited to determining the order of one fragment of DNA per reaction, up to a maximum length of ~700 bases. NGS platforms can sequence millions of DNA fragments in parallel in one reaction, yielding enormous amounts of data [8].
Illumina Sequencing Technology Massive parallel sequencing with Sequencing by synthesis (SBS) chemistry, is now adapted over wide regions as they detect each single base as they are incorporated into the new strands of DNA as they lengthen gradually.
Method: The Illumina sequencing with SBS is done in 4 steps, namely, sample preparation, cluster generation, sequencing and data analysis. The sample preparation could be done by various different methods. Reduced cycle amplification is widely used, through which additional sites are introduced like the sequencing binding sites and regions which are complementary to those strands are added. During cluster generation, each fragment of the molecule is isothermally amplified and placed in a flow slide which consists of several lanes with two types of oligos. The first fragment of oligo is hybridized and then a polymerase enzyme is used to create the complimentary strand of the hybridized fragment. The complementary strand is amplified by the process of 'bridge amplification'. The same procedure is then repeated several times from the thousands and thousands of fragments and they are done in many clusters. The 3' end of the fragment is blocked to avoid any other binding of primers to it. The nucleotides attach and bind to their respective complementary base pairs by competitive binding. After binding, the strand is activated or excited by a fluorescence signal which is emitted. This particular process is known as a sequence by synthesis, where many clusters of the DNA fragments are sequenced in a massively parallel fashion. At last, the data analysis is when all the sequences are read and aligned and it is put together for identification of any abnormalities in the nucleotide sequence like mutations or other disorientations. They use a base space sequence hub to store, analyze and process these data for future use and researches [10].
Bind to primer PCR extension
1*1
Cluster formation
Figure 2. Outline of Illumina genome analyzer sequencing process. (1) Adaptors are annealed to the ends of sequence fragments. (2) Fragments bind to primer-loaded flow cell and bridge PCR reactions amplify each bound fragment to produce clusters of fragments. (3) During each sequencing cycle, one fluorophore attached nucleotide is added to
И ..
иуЛГ
■ и ■ ■ ■ /
Dissociation
Sequencing Signal scanning
the growing strands. Laser excites the fluorophores in all the fragments that are being sequenced and an optic scanner collects the signals from each fragment cluster. Then the sequencing terminator is removed and the next sequencing cycle starts [10].
NSG in the field of oncology for a Personalized treatment regimen
Nearly for the past decade, NSG has been used in oncology mainly to determine the cancer mutations which lead to the unstoppable rapid cellular replication.
Specifically, many new mutations were identified which caused cancer and this information will help to prepare a personalized treatment regimen for the patient. These novel oncogenic mutations were found in a wide spectrum of cancer, which includes lung cancer [11] - small cell carcinoma [12] and large cell carcinoma differentiation [11]; metastatic small-cell gallbladder neuroendocrine carcinoma [13], clear cell renal cell carcinoma [14], prostate cancer [15], breast cancer [16], transitional cell carcinoma of the bladder [17] and also in various types of leukemia [18; 19; 20].
Various studies have shown the specific associations of a particular mutant gene with one or many malignancies. Mutations occurring in the tumor suppressor genes, which due to loss of function leads to increase cancer risk and both the alleles of a tumor suppressor gene must be lost for the expression of disease. Some of the well-known associations of mutant tumor suppressor genes include APC gene mutation with colorectal cancer [21; 22]; BRCA1 and BRCA2 gene mutation with breast cancer [23], ovarian cancer [24] and pancreatic cancer [25]; CDKN2A mutation blocks transmission from G1 to S phase and it is associated with melanoma [26] and
The introduction of the concept of precision tumor therapy into clinical practice may result in a transition to the so-called tumor-type agnostic therapy, in which, when prescribing a drug, one is guided not by anatomical localization or histological type of tumor, but by the presence in it of a drug-specific and common for different tumors biomarker, revealed as a result of genomic research of a tumor of an individual patient. In other words,
pancreatic cancer [27]; DCC mutation is associated with colon cancer [28]; SMAD4 (DPC4) mutation with pancreatic cancer [29]; MEN1 mutation with multiple endocrine neoplasia type 1 [30]; mutant NF1 is connected with neurofibromatosis type 1 [31]; mutant NF2 associated with neurofibromatosis type 2 [32]; PTEN mutation which is the gene of negative regulator of PI3k/AKT pathway, associated with prostate cancer [33], breast cancer [34] and endometrial cancer [35]; Rb mutation inhibits E2F and blocks transition from G1 to S1 phase, connected to malignancies like retinoblastoma [36] and osteosarcoma [37]; mutation on TP53 can cause a wide range of cancers [38], mostly all the human cancer types could be developed, but particularly Li-Fraumeni syndrome- multiple malignancies at an early age (SBLA cancer syndrome: sarcoma, breast cancer, leukemia, adrenal gland cancer) [39]; mutant TSC1 and TSC2 producing hamartin protein and tuberin protein respectively causes tuberous sclerosis [40]; mutant VHL gene which normally inhibits hypoxia-inducible factor 1a is associated with von Hippel-Lindau disease [41]; WT1 mutation is associated with Wilms tumor (neuroblastoma) [42] The data obtained by sequencing the DNA of different tumors can serve as a basis for the creation of new molecular-oriented drugs. When a common mutation is identified and its significance for tumor progression is proven, it is possible to create, synthetically or biotechnologically, a drug that interacts with the corresponding mutated protein and blocks its action. Table 1 shows some of the targets set up in this way and the molecular-oriented drugs designed to target these targets, already approved for use or in clinical trials.
within the framework of this concept, it is assumed that indications for the use of the drug will indicate not the type of tumor (for example, NSCLC), but the presence of a certain biomarker, which allows the drug to be used in any tumor if the expression of this marker is detected in it [43].
In the past year, this new concept of cancer drug therapy has come to fruition with FDA approval for new indications for previously approved drugs.
Table 1
Targets for the creation of new molecular-associated drugs, selected based on DNA sequencing
Targets Drugs
FGFR (fibroblast growth factor receptor) Erdafinitib
CDK4 / 6 (cyclin dependent kinases 4 and 6) Palbocinib, ribociclib, abemacyclib
CD19 and CD3 (antigens of the surface membranes of B-lymphocytes and T-cells) Blinatumemab
DLL3 (small cell lung cancer cell antigens) Zovalpituzumab tesirin
CCR2 (C-C chemokine receptor 2) CCX 272
The immunotherapy drug pembrolizumab, originally approved for the treatment of melanoma and NSCLC patients, has been accelerated by the FDA for the treatment of any tumors that exhibit high levels of microsatellite instability (MCH) or a defect in the mismatch repaire (MMR) system responsible for the recognition and removal of mismatched bases formed as a result of errors in the process of DNA replication [43]. The operation of this system is regulated by the expression of 6 genes (MSH2, MLH1, PMS2, MSH3, MSH6, and MLH3), mutations of which lead to a defect in MMR (dMMR), the appearance of a large number of mutations, and the synthesis of non-functional proteins. Breakdowns in the repair system are characterized by the accumulation of large amounts of microsatellites in DNA, which are short nucleotide sequences of 1-5 bases, repeating up to several tens of times.
Microsatellites are also found in normal conditions, but at dMMR their number increases tens to hundreds of times. Tumors with a high MCH are characterized by lymphoid infiltration, a large number of somatic mutations, and increased formation of neoantigens, which can serve as targets for the immune system and enhance the immune response [44].
The classical method for determining MCH is PCR, which amplifies microsatellite repeats in DNA, and the level of genome instability is determined by comparing their length between tumor and normal cells. To diagnose dMMR, an immunohistochemical study is used, when the expression of proteins MSH2, MLH1, PMS2, MSH6 is studied in the tumor. If at least one protein is not stained, deficiency of MMR. In recent years, it has become possible to determine the MCH and dMMR using NGS.
When examining 32 types of tumors with NGS 12019, dMMR was detected in 24 types of tumors, while a dMMR frequency> 2% was recorded in 11 types of tumors (endometrial cancer, cervix, stomach, small intestine, prostate and thyroid gland, bile duct, liver, CRC, uterine sarcoma, neuroendocrine tumors). It was noted that in these tumors dMMR was observed twice as often in stage I - III tumors as compared with stage IV tumors. It is estimated that 60,000 patients are diagnosed with dMMR tumors each year in the United States. It is believed that in these patients, checkpoint inhibitors can be used with effect, including in cases refractory to other therapy [45].
The role of high MCH in the efficacy of pembrolysumab was discovered by chance. In a clinical trial of pembrolizumab, out of 19 patients with CRC, the effect was recorded in only one patient - a complete regression lasting more than
3 years. In a retrospective study of the genome of this tumor, it was found that it has a high level of MCH due to dMMR.
It was hypothesized that since dMMR leads to an increase in somatic mutations, a large number of tumor neoantigens appear in the tumor, which are a target for cytotoxic T lymphocytes, which should lead to the induction of an immune antitumor response. However, in tumors with a high MCH, there is an overexpression of PD-1 and PD-L1, which prevents this. Therefore, the blockade of checkpoint immune points should enhance the efficiency of the immune response to the tumor [44; 46].
This hypothesis was confirmed in a comparative clinical study, which recorded a high efficacy of pembrolizum in colorectal cancer patients with dMMR, while almost completely ineffective with preserved MMR. Full exome sequencing of DNA revealed 1782 mutations in tumors with dMMR, and 73 in tumors with preserved MMR [46].
D. Le et al. used pembrolizumab in 86 previously treated patients with 12 types of dMMR tumors. An objective effect was registered in 46% of cases, including a complete regression in 21% with a median 2-year survival rate of 53%, while the effectiveness of the drug was practically the same in all types of tumors [45].
In several clinical studies of KET-NOTE, which included a total of 415 previously treated patients with 15 types of different common tumors in 149 immunochemically or and a high MCH or dMMR was detected by PCR. The use of pembrolizumab in these patients resulted in complete or partial regression in 39.6% of patients (complete regression in 7.4%). In 78% of cases, remissions lasted more than 6 months. These studies also show that the frequency of the objective effect was practically the same in tumors of different types [43; 44].
The results of these studies have served as the basis for the approval of the use of pembrolizumab in any solid tumor (both adults and children) with a high MCH or dMMR. For the first time in history, the indication for the use of the drug was not a tumor of a certain localization, but the presence of a biomarker. Moreover, this is the first time that a drug has been approved for use without data from randomized clinical trials, including in children [43; 47].
Somewhat later, the use of another immunotherapeutic drug, nivulumab, was approved for the treatment of colorectal cancer when these markers are registered in the tumor. The use of nivolumab in patients with CRC with high MCH or dMMR and progression after previous chemotherapy with fluoropyrimidines, oxaliplatin, irinotecan was effective in 28% of cases. The results
of this study allowed the FDA to authorize the use of nivolumab in the progression of colorectal cancer when these markers are found in tumors [43].
The results of various studies have given grounds to consider MCH and dMMR as reliable predictors of the effectiveness of checkpoint inhibitors [46]. It is believed that the use of the concept of tumor type-agnostic therapy will provide an opportunity for effective treatment in patients with rare tumors.
It should be noted, however, that the frequency of dMMR varies greatly in different types of tumors. MCH is found in more than 10% of cases in thyroid cancer, endometrial cancer, stomach cancer, colorectal cancer, hepatocellular cancer, melanoma. In other tumors, MSI is much less common (for example, in renal cell carcinoma and head-neck cancer in 2-3%, in breast cancer, in lung cancer even less often). There is evidence that the level of MCH and dMMR in the tissue of metastases is lower than in the primary tumor [44; 46].
The tumor type-agnostic concept began to be applied not only to change indications for already existing drugs, but also in the clinical study of new targeted drugs. An example is the drug larotrectinib (LOXO-1), which has a fusion protein (NTRK) as a target, which is formed by fusion of the tropomyosin receptor kinase (Trk) gene with other genes (ETV6, LMNA, TPM3). It was found that this protein induces cell proliferation by activating signaling pathways. Such a genetic disorder develops in 0.51% of the most common malignant neoplasms, but is typical for some rare oncopathologies: salivary gland cancer, childhood fibrosarcoma, and juvenile breast cancer [47].
Interest in the drug appeared after the report on the results of the use of larotrectinib in 41-year-olds D.B. Cormanher patient with metastases of soft tissue sarcoma in the lungs. Oral administration of larotrectinib led to a rapid complete tumor regression (a decrease in tumor size was recorded after the 1st cycle of taking the drug, complete regression after the 4th cycle).
At the ASCO Congress in 2017, the first results of a clinical study of larotrectinib were reported in patients with various tumors, in which the presence of the NTRK fusion protein was proven by different methods. The study included 55 patients (aged 4 months - 76 years) with 17 types of tumors. An objective effect was observed in 76% of cases in 12 types of tumors [43, 45]. In October 2018, the FDA approved the use of the drug for any tumors in the presence of the Trk / ETV6 fusion gene, LMNA, TPM3, or NTRK fusion protein in the tumor.
Another example is studies that investigated the efficacy of fibroblast growth factor receptor (FGFR) inhibitors in various tumors with FGFR2 / 3 confluent protein. A positive effect was recorded in
various tumors - cholangiocellular cancer, bladder cancer and gliomas [48].
CONCLUSION
Personalized therapy will be more valuable and effective to patients battling cancer, as it is a pathology that presents with a vast variability among different individuals. Gene sequencing technique allows researchers and physicians to initiate bench to bedside implementations to diagnose, for prognosis, and treat cancer more effectively compared to the standard methods [49]. Every research dedicated to the improvisation of cancer treatment takes us one step forward to a cure in the near future.
Conflict of interest. The authors have no conflict of interests to declare.
Конфликт интересов. Авторы заявляют об отсутствии конфликта интересов.
Финансирование. Работа выполнена при финансовой поддержке государственного задания Министерства науки и высшего образования РФ № ФЗЭГ-2020-0060 в области научных исследований по теме «Алгоритмы молекуляр-но-генетической диагностики злокачественных новообразований и подходы к их таргетной терапии с использованием клеточно-генетиче-ских технологий». и частично поддержан VI Программа развития Крымского федерального университета им. В.И. Вернадского на 2015 -2024 гг.
Funding. This work was financially supported by state task No FZEG-2020-0060 of the Russian Ministry of Science in the feld of scientifc research on the topic "Algorithms for molecular genetic diagnosis of malignant neoplasms and approaches to their targeted therapy using cellular and genetic technologies" and partially supported by the V.I. Vernadsky Crimean Federal University Development Program for 2015 - 2024.
REFERENCES / ЛИТЕРАТУРА
1. Sung H., Ferlay J., Siegel R. L., Laversanne M, Soerjomataram I., Jemal A., Bray F. Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries. CA Cancer J Clin. 2021;71(3):209-249. doi:10.3322/caac.21660.
2. Hastings K. G., Boothroyd D. B., Kapphahn K., Hu J., Rehkopf D. H., Cullen M. R., Palaniappan L. Socioeconomic Differences in the Epidemiologic Transition From Heart Disease to Cancer as the Leading Cause of Death in the United States, 2003 to 2015: An Observational Study. Ann Intern Med. 2018 Dec 18;169(12):836-844. doi:10.7326/M17-0796.
3. Collier A., Meney C., Hair M., Cameron L., Boyle J. G. Cancer has overtaken cardiovascular disease as the commonest cause of death in Scottish type 2 diabetes patients: A population-based study (The Ayrshire Diabetes Follow-up Cohort study). J Diabetes Investig. 2020;11(1):55-61. doi:10.1111/ jdi.13067.
4. Gupta S., Harper A., Ruan Y., Barr R., Frazier A. L., Ferlay J., Steliarova-Foucher E., Fidler-Benaoudia M. M. International Trends in the Incidence of Cancer Among Adolescents and Young Adults. J Natl Cancer Inst. 2020;112(11):1105-1117. doi:10.1093/jnci/djaa007.
5. Behjati S., Tarpey P. S. What is next generation sequencing? Arch Dis Child Educ Pract Ed. 2013;98(6):236-8. doi:10.1136/ archdischild-2013-304340.
6. Welch J. S., Westervelt P., Ding L. Use of Whole-Genome Sequencing to Diagnose a Cryptic Fusion Oncogene. JAMA. 2011;305(15):1577-1584. doi:10.1001/jama.2011.497
7. Tipu H. N., Shabbir A. Evolution of DNA sequencing. J Coll Physicians Surg Pak. 2015 Mar;25(3):210-5.
8. Bunnik E. M., Le Roch K. G. An Introduction to Functional Genomics and Systems Biology. Adv Wound Care (New Rochelle). 2013;2(9):490-498. doi:10.1089/wound.2012.0379.
9. Slatko B. E., Gardner A. F., Ausubel F. M. Overview of Next-Generation Sequencing Technologies. Curr Protoc Mol Biol. 2018;122(1):e59. doi:10.1002/cpmb.59.
10. Lu Yn., Shen Y., Warren W., Walter R. Next Generation Sequencing in Aquatic Models. 2016. doi:10.5772/61657.
11. Rekhtman N., Pietanza M. C., Hellmann M. D., Naidoo J. Next-Generation Sequencing of Pulmonary Large Cell Neuroendocrine Carcinoma Reveals Small Cell Carcinoma-like and Non-Small Cell Carcinoma-like Subsets. Clin Cancer Res. 2016;22(14):3618-29. doi: 10.1158/1078-0432. CCR-15- 2946.
12. McFadden D. G., Papagiannakopoulos T., Taylor-Weiner A. Genetic and clonal dissection of murine small cell lung carcinoma progression by genome sequencing. Cell. 201413;156(6):1298-1311. doi: 10.1016/j.cell.2014.02.031.
13. Li M., Liu F., Zhang Y., Wu X. Whole-genome sequencing reveals the mutational landscape of metastatic small-cell gallbladder neuroendocrine carcinoma (GB-SCNEC). Cancer Lett. 2017;391:20-27. doi: 10.1016/j. canlet.2016.12.027.
14. Meng H., Jiang X., Cui J., Yin G., Shi B., Liu Q., Xuan H., Wang Y. Genomic Analysis Reveals Novel Specific Metastatic Mutations in Chinese
Clear Cell Renal Cell Carcinoma. Biomed Res Int. 2020;2020:2495157. doi: 10.1155/2020/2495157.
15. Liang C., Niu L., Xiao Z., Zheng C., Shen Y., Shi Y., Han X. Whole-genome sequencing of prostate cancer reveals novel mutation-driven processes and molecular subgroups. Life Sci. 2020;254:117218. doi: 10.1016/j.lfs.2019.117218.
16. Chang Y. S., Chang C. M., Lin C. Y., Chao D. S., Huang H. Y., Chang J. G. Pathway Mutations in Breast Cancer Using Whole-Exome Sequencing. Oncol Res. 2020;28(2):107-116. doi: 10.3727/0965 04019X15698362825407.
17. Pan H., Xu X., Wu D., Qiu Q., Zhou S., He X., Zhou Y., Qu P., Hou J., He J., Zhou J. Novel somatic mutations identified by whole-exome sequencing in muscle- invasive transitional cell carcinoma of the bladder. Oncol Lett. 2016;11(2):1486-1492. doi: 10.3892/ol.2016.4094.
18. Kiel M. J., Velusamy T., Rolland D. Integrated genomic sequencing reveals mutational landscape of T-cell prolymphocytic leukemia. Blood. 2014;124(9):1460-72. doi: 10.1182/ blood-2014-03-559542.
19. Ding L., Ley T. J., Larson D. E. Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature. 2012;481(7382):506-10. doi: 10.1038/nature10738.
20. Mosquera Orgueira A., Rodríguez Antelo B., Díaz Arias J. Á., Díaz Varela N., Alonso Vence N., González Pérez M. S., Bello López J. L.. Novel Mutation Hotspots within Non-Coding Regulatory Regions of the Chronic Lymphocytic Leukemia Genome. Sci Rep. 2020;10(1):2407. doi: 10.1038/ s41598-020-59243-5.
21. Fodde R. The APC gene in colorectal cancer. Eur J Cancer. 2002;38(7):867-71. doi: 10.1016/ s0959-8049(02)00040-0.
22. Ying R., Wei Z., Mei Y., Chen S., Zhu L. APC gene 3'UTR SNPs and interactions with environmental factors are correlated with risk of colorectal cancer in Chinese Han population. Biosci Rep. 2020 Mar 27;40(3):BSR20192429. doi: 10.1042/BSR20192429.
23. Mahdavi M., Nassiri M., Kooshyar M. M., Vakili-Azghandi M., Avan A., Sandry R., Pillai S., Lam A. K., Gopalan V. Hereditary breast cancer; Genetic penetrance and current status with BRCA. J Cell Physiol. 2019;234(5):5741-5750. doi: 10.1002/ jcp.27464.
24. Moschetta M., George A., Kaye S. B., Banerjee S. BRCA somatic mutations and epigenetic BRCA modifications in serous ovarian cancer. Ann Oncol. 2016;27(8):1449-55. doi: 10.1093/annonc/ mdw142.
25. Kowalewski A., Szylberg L, Saganek M., Napiontek W., Antosik P., Grzanka D. Emerging strategies in BRCA-positive pancreatic cancer. J
Cancer Res Clin Oncol. 2016;144(8):1503-1507. doi:10.1007/s00432-018-2666-9.
26. Leachman S. A., Lucero O. M., Sampson J. E., Cassidy P., Bruno W., Queirolo P., Ghiorzo P. Identification, genetic testing, and management of hereditary melanoma. Cancer Metastasis Rev. 2017;36(1):77-90. doi: 10.1007/s10555- 017-9661-5.
27. Zhen D. B., Rabe K. G., Gallinger S. BRCA1, BRCA2, PALB2, and CDKN2A mutations in familial pancreatic cancer: a PACGENE study. Genet Med. 2015;17(7):569-77. doi: 10.1038/ gim.2014.153.
28. Gotley D. C., Reeder J. A., Fawcett J., Walsh M. D., Bates P., Simmons D. L., Antalis T. M. The deleted in colon cancer (DCC) gene is consistently expressed in colorectal cancers and metastases. Oncogene. 1996;13(4):787-95. PMID: 8761300.
29. Wang F., Xia X., Yang C., Shen J., Mai J., Kim H. C., Kirui D., Kang Y., Fleming J. B., Koay E. J., Mitra S., Ferrari M., Shen H. SMAD4 Gene Mutation Renders Pancreatic Cancer Resistance to Radiotherapy through Promotion of Autophagy. Clin Cancer Res. 2018;24(13):3176-3185. doi: 10.1158/1078-0432.CCR-17- 3435.
30. Carroll R. W. Multiple endocrine neoplasia type 1 (MEN1). Asia Pac J Clin Oncol. 2013;9(4):297-309. doi: 10.1111/ajco.12046.
31. Kang E., Kim Y. M., Seo G. H. Phenotype categorization of neurofibromatosis type I and correlation to NF1 mutation types. J Hum Genet. 2020;65(2):79-89. doi: 10.1038/s10038-019-0695-0.
32. Asthagiri A. R., Parry D. M., Butman J. A., Kim H. J., Tsilou E. T., Zhuang Z., Lonser R. R. Neurofibromatosis type 2. Lancet. 2009;373(9679):1974-86. doi:10.1016/S0140-6736(09)60259-2.
33. Wise H. M., Hermida M. A., Leslie N. R. Prostate cancer, PI3K, PTEN and prognosis. Clin Sci (Lond). 2017;131(3):197-210. doi: 10.1042/ CS20160026.
34. Ngeow J., Sesock K., Eng C. Breast cancer risk and clinical implications for germline PTEN mutation carriers. Breast Cancer Res Treat. 2017;165(1):1-8. doi: 10.1007/s10549-015-3665-z.
35. Bian X., Gao J., Luo F., Rui C., Zheng T., Wang D., Wang Y., Roberts T. M., Liu P., Zhao J. J., Cheng H. PTEN deficiency sensitizes endometrioid endometrial cancer to compound PARP-PI3K inhibition but not PARP inhibition as monotherapy. Oncogene. 2018;37(3):341-351. doi: 10.1038/ onc.2017.326.
36. Mendoza P. R., Grossniklaus H. E. The Biology of Retinoblastoma. Prog Mol Biol Transl Sci. 2015;134:503-16. doi: 10.1016/ bs.pmbts.2015.06.012.
37. Czarnecka A. M., Synoradzki K., Firlej W., Bartnik E., Sobczuk P., Fiedorowicz M., Grieb P., Rutkowski P. Molecular Biology of Osteosarcoma. Cancers (Basel). 2020;12(8):2130. doi: 10.3390/ cancers12082130.
38. Leroy B., Anderson M., Soussi T. TP53 mutations in human cancer: database reassessment and prospects for the next decade. Hum Mutat. 2014;35(6):672-88. doi: 10.1002/humu.22552.
39. Guha T., Malkin D. Inherited TP53 Mutations and the Li-Fraumeni Syndrome. Cold Spring Harb Perspect Med. 2017;7(4):a026187. doi: 10.1101/ cshperspect.a026187.
40. Salussolia C. L., Klonowska K., Kwiatkowski D. J., Sahin M. Genetic Etiologies, Diagnosis, and Treatment of Tuberous Sclerosis Complex. Annu Rev Genomics Hum Genet. 2019;20:217-240. doi: 10.1146/annurev-genom-083118- 015354.
41. Lenglet M., Robriquet F., Schwarz K. Identification of a new VHL exon and complex splicing alterations in familial erythrocytosis or von Hippel- Lindau disease. Blood. 2018;132(5):469-483. doi: 10.1182/blood-2018-03- 838235.
42. Valind A., Wessman S., Pal N., Karlsson J., Jonson T., Sandstedt B., Gisselsson D. Convergent evolution of 11p allelic loss in multifocal Wilms tumors arising in WT1 mutation carriers. Pediatr Blood Cancer. 2018 Nov;65(11):e27301. doi: 10.1002/pbc.27301.
43.Le D.T., Durham J.N., Smith K.N., Wang H., Barlett B., Aulakh L.K., Lu S., Kemberling H., Wilt C., Luber B.S., Wong F., Azaf N.S., Rucki A.A. Mismatch repair deficiency predicts response of solid tumors to PD-1 blockade. Science. 2017; 357: 409-413.
44. Lemery S., Keegan P., Pazdur R. Feist FDA approval agnostic of cancer site - when a biomarker defines the indication. N. Engl. J. Med. 2017; 377(15): 1409-1412. doi: 10.1056/NEJMp1709960.
45. Garber K. In a maior shift, cancer drugs go «tissue-agnostic». Science. 2017; 356(6343): 11111112. doi: 10.1126/ science.356.6343.1111.
46. Dudley J. C., Lin M. T., Le D. T., Escherman R. Microsatellite instability as biomarker for PD-1 blockade. Clin. Cancer Res. 2016; 22(4): 813-820. doi: 10.1156/1078-0432.ccr-15-1678.
47. Berger S., Nartens U.M., Bochum S. Larotrectinib (LOXO-101). Rec. Res. Cancer Res. 2018; 211: 141-151.
48. Hyman D. M., Taylor B. S., Baselga J. Implementing genomic-driven oncology. Cell. 2017; 168(2): 584-599. doi: 10.1016/j:cell.2016.12.015.
49. Hamis S., Powathil G. G., Chaplain M. A. J. Blackboard to Bedside: A Mathematical Modeling Bottom-Up Approach Toward Personalized Cancer Treatments. JCO Clin Cancer Inform. 2019;3:1-11. doi: 10.1200/CCI.18.00068.
