OBJECTIVE:Describe the structure of pathogenic germline variants and clinical and anatomical features in colorectal cancer patients in Moscow.MATERIAL AND METHODS:The whole genome sequencing results of patients with suspected hereditary cancer syndrome were evaluated. All identified genetic variants were validated using Sanger sequencing.RESULTS:The study included 238 patients with colorectal cancer, 41/238 (17.2%) patients have pathogenic germline variants associated with hereditary cancer syndromes or increased cancer risk. Lynch syndrome accounts for 8% of all colorectal cancer cases (19/238), and familial adenomatous polyposis - 1.7% (4/238). 5 new genetic variants were described for the first time in a Russian colorectal cancer patients: MLH1 c.1921dup (p.Leu641fs), APC c.2929C>T (p.Gln977Ter), PMS2 c.327del (p.Ala110LeufsTer2), MSH2 c.1857dup (p. Val620CysfsTer24), ATM c.895G>T (p.Glu299Ter). In 197 of 238 patients, no significant variants were identified or variants with an uncertain clinical underlying cause were identified.CONCLUSION:According to the results of the study, an earlier manifestation of a malignant neoplasm and a more frequent occurrence of high-grade carcinomas in the presence of pathogenic germline mutations were noted compared to the group of patients without clinically significant varianrs, while in the group with identified mutations, the frequency of regional and distant metastasis was not increased.

Background: Germinal pathogenic variants are the cause of the development of hereditary cancer syndromes (HCS). Various genetic tests are used for HCS detect, from the «frequent» mutations of one or several genes analysis to the full-length gene sequence, next-generation sequencing (NGS) based panel, whole exome (WES) or whole genome sequencing (WGS).There are some HCS cases with atypical clinical manifestations and the family history does not allow one to suspect a specific HCS and limit oneself to the study of only one or a few genes. Conducting research using NGS to assess the selected sample of cancer patient’s genetic characteristics has revealed atypical HCS cases.Aim: To present the WGS diagnosis results for two atypical hereditary tumor syndromes cases.Materials and methods: DNA isolation was performed using Qiagen DNA Isolation kit. WGS for all samples was performed at DNBSEQ-T7 (MGI) and DNBSEQ-G400 (MGI) sequencing platforms using PCR-free protocol with average sample coverage 30x. A standard bioinformatics analysis pipeline was implemented for all the samples data processing.Potential clinically relevant variants were validated using Sanger sequencing. For all patients was received signed a written consent.Results: In the first case report, a pathogenic variant in the TP53 gene was identified: c. 637C > T, p. Arg213Ter, rs397516436, and Li – Fraumeni syndrome was confirmed. In the second case, we detected two pathogenic variants carrier — BRCA2: c. 6644_6647del, p. Tyr2215SerfsTer13, rs80359616 and MSH2: c. 1906G > C, p. Ala636Pro, rs63750875 associated with hereditary breast and ovarian cancer and hereditary colorectal cancer (Lynch syndrome).Conclusion: NGS, including WGS makes it easier to identify all clinically significant germline variants associated with hereditary cancer syndromes in cancer patients, as well as to trace their segregation in relatives.

Cowden syndrome is a rare disease characterized by multiple hamartomas and increased breast, thyroid, kidney and uterine neoplasm risk. The lifetime breast cancer risk for patients with Cowden syndrome is 85 %, with an average age of diagnosis between 38 and 46 years. The diagnostic criteria for Cowden syndrome have been established by the International Cowden Consortium (ICC) and the National Comprehensive Cancer Network (NCCN), and are regularly revised, but the diagnosis of Cowden syndrome remains difficult due to the variety of phenotypic and clinical features of the disease. At the same time, the genetic variants associated with Cowden syndrome analysis is not a standard for patients with breast cancer.Objective: To demonstrate the non‑BRCA hereditary breast cancer detection using whole genome sequencing on the Cowden syndrome clinical case example.Materials and methods: The article describes a clinical case of a 37‑year‑old female patient with breast cancer, normal intelligence and phenotype, structural abnormalities of the thyroid gland (multinodular goiter). Whole genome sequencing was used to identify clinically significant genetic variants associated with hereditary tumor syndromes.Clinical case: The article presents a brief literature review on the clinical presentation of Cowden syndrome and indications for its molecular diagnosis. Also, the presented clinical case describes patient R., 37 years old female with breast cancer, who underwent treatment in the City Clinical Oncological Hospital № 1 of the Moscow City Health Department in 2021. The patient was fully examined and enrolled in the whole genome sequencing project under the Order № 69 of Moscow Healthcare Department dated February 1, 2021 «Oncogenetic research organization in Moscow». The results revealed a pathogenic variant in the PTEN gene, previously associated with Cowden syndrome.Conclusion: The use of whole genome sequencing allows to identify hereditary tumor syndromes, the clinical manifestation of which may be breast cancer.

ЦЕЛЬ ИССЛЕДОВАНИЯ Проанализировать результаты пренатального скрининга с применением неинвазивного пренатального тестирования (НИПТ) в Москве за период с 01.04.20 по 30.09.20. Оценить преимущество использования НИПТ перед комбинированным пренатальным скринингом в первом триместре беременности. МАТЕРИАЛ И МЕТОДЫ Проанализирован 5181 образец крови в период с 01.04.20 по 30.09.20. Неинвазивное пренатальное тестирование осуществляли методом полногеномного секвенирования. Для дальнейшего генетического исследования материала плода после инвазивных процедур проводили кариотипирование и молекулярно-генетический анализ. Для оценки эффективности сравнивали результаты, полученные при НИПТ, с результатами инвазивной пренатальной диагностики у пациенток в группе высокого риска и в группе риска 1:101—1:2500. РЕЗУЛЬТАТЫ Высокий риск хромосомных аномалий плода в отношении частых анеуплоидий по результатам НИПТ определен в 72 случаях из 5181:50 случаев трисомии 21, 17 случаев трисомии 18 и 5 случаев трисомии 13. Отмечено, что на уровень фетальной фракции влияют масса тела, индекс массы тела пациенток, наличие трисомий, пол плода. ВЫВОДЫ По предварительным данным, внедрение неинвазивного пренатального тестирования в практическое здравоохранение может снизить число ложноотрицательных случаев хромосомной патологии плода в группе риска 1:101—1:2500, а также потенциально уменьшить число инвазивных вмешательств в группе высокого риска. Вместе с тем в связи с небольшим размером выборки требуются дальнейшие исследования.

Non-invasive prenatal testinging (NIPT) is a relatively new method aimed at detecting fetal chromosomal aneuploidies by analyzing extracellular fetoplacental DNA in the blood of a pregnant woman. NIPT has high sensitivity and specificity, and many professional communities now recommend its use as a screening method. Since its introduction into clinical practice in Hong Kong in 2011, NIPT has expanded rapidly around the world. The experience of various countries in organizing non-invasive prenatal testing is described in this article. Key words: NIPT, non-invasive prenatal testing, extracellular fetoplacental DNA, prenatal screening, prenatal diagnosis, invasive prenatal diagnosis, aneuploidy

Congenital malformations, chromosomal and monogenic disease play a significant role in perinatal mortality and child disability. According to the early prenatal screening results in the Russian Federation in 2018, the overall ratio of chromosomal anomaly prevalence is 1:250–1:300. Currently aneuploidy risk is calculated by using indirect biochemical and ultrasound markers, that have low sensitivity and specificity which can cause false positives and false negative results leading to unreasonable invasive procedures or missing chromosomal anomalies. It is well known that cell-free fetal DNA is detected in maternal blood. Whole‐genome sequencing based non-invasive prenatal testing (NIPT) can detect fetal chromosomal aneuploidy with high sensitivity as early as 10 weeks into pregnancy. The accuracy of determining fetal sex is also high: sensitivity and specificity are 98,9% and 99,9% respectively. Implementing molecular technology into clinical practice is required to improve prenatal diagnosis in the Russian Federation, icluding Moscow. Integration of NIPT to analyse cell-free fetal DNA will increase the efficiency of fetal chromosomal anomalies’ detection. However, there are some legal and ethical aspects to consider when integrating a new technology for wide-spread use. This review reveals arguable issues of NIPT integration into widespread clinical practice and possible ways of solving those issues. Key words: NIPT, noninvasive prenatal test, prenatal screening, fetal sex, invasive prenatal diagnosis, X-linked disease, chromosomal anomaly, chromosomal microarray analysis