Browsing by Subject "exome sequencing"
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(2019)Uterine leiomyomas are common benign smooth muscle tumors. They are a major gynecological problem affecting women’s health and contribute to a significant burden on national health expenditure. They can be classified based on their histopathology into conventional, and histopathological variants. Most of the conventional tumors exclusively harbor one of the three drivers (MED12 mutations, HMGA2 overexpression, and biallelic FH inactivation). Based on the genetic background, histopathological subtypes differ from each other and from conventional leiomyomas. Although histopathological variants are considered benign, they share some resemblance to malignant uterine leiomyosarcomas. The overall aim of the thesis was to characterize the mutational landscape of histopathological leiomyoma variants using exome sequencing. The specific aims were, to identify new causative mutations in the histopathological variants and within subtypes, and to analyze pathogenic cancer census gene mutations within the variants. Exome sequencing was performed on 35 tumors representing variant histopathology (14 highly cellular, 12 bizarre nuclei, and 9 mitotically active tumors). The sequences were analyzed using BasePlayer software. Mutations were filtered through the designed pipeline using gnomAD, and COSMIC controls. Interesting findings were validated using Sanger sequencing. Exome data analysis of the highly cellular and bizarre nuclei tumors separately resulted in 10 and 17 different mutations in each subtype, respectively. They were found to be pathogenic by in silico predictions. Analysis of all histopathological variants including mitotically active tumors did not reveal any frequently mutated candidate genes. The tumors harbored somatic mutations in 98 genes related to cancer. A mutation in TP53 was found in one bizarre nuclei sample. Specific tumors harbored multiple cancer-related mutations indicating their malignant potential. The highly cellular tumors had the least frequent amount of causative mutations, indicating that the tumorigenesis mechanisms are probably other than missense mutations or small indels in exomes. Tumors with bizarre nuclei displayed a noticeably larger amount of possible pathogenic mutations, in both cancer census and exome analysis, suggesting possible cancerous tendency. This was also supported by the TP53 finding, a gene associated with uterine leiomyosarcomas. The histopathological subtypes pathogenesis is conceivably caused by larger genomic alterations, epigenetic variations or intronic mutations that remain to be found. Tumors with frequent cancer census mutations might harbor malignant potential. Understanding the etiology of these tumors is needed for better diagnostics and possible targeted treatments
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(2021)Skeletal dysplasias are a group of rare monogenic bone disorders affecting joints and the skeleton. An increasing number of gene defects have been associated with skeletal dysplasias, but many cases remain without a known cause or a clear diagnosis. Exome sequencing data of the family with two siblings affected with an undiagnosed type of bone dysplasia was examined in this study with the aim of determining the genetic cause behind the phenotype. The causal variant was assumed to be in a novel disease-causing gene, since a previously performed gene panel of skeletal disease-causing genes had not revealed any positive results. The search for potential rare pathogenic variants in genes linked to the skeleton was done with VarAFT filtering software. The search revealed a short list of candidate variants confirmed first with Broad Institute’s Integrative Genomics Viewer (IGV) and then with targeted Sanger sequencing. Conservation analysis on the affected amino acids, in silico functional analysis on the variants and a comprehensive literature review on all candidate genes were performed to evaluate the likelihood of them being the variant behind the phenotype. A shortlist of three genes were obtained with the analyses, with one of them seeming to be the most likely candidate. However, to assuredly identify the disease-causing variant, further testing should be performed. Functional analyses should be done to test the functions of the proteins encoded by the candidate genes and the consequences of the pathogenic variants.
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(2023)Geenien sekvensointiteknologian kehittyessä on alettu pohtia laajennetun kantajuusseulonnan järjestämistä julkisin varoin. Riskissä olevien pariskuntien tunnistaminen voisi luoda parempaa lisääntymisautonomiaa sekä voi mahdollistaa inhimillisten ja taloudellisten kustannusten vähentämistä. Esimerkiksi American College of Medical Genetics (ACMG) on muodostanut laajennetusta kantajuusseulonnasta suosituksia, joiden mukaan tarpeeksi vakavia ja yleisiä peittyvästi periytyviä sairauksia tulisi seuloa halukkailta raskautta suunnittelevilta pariskunnilta. Tutkimuksessa selvitettiin 140 geenin (autosomaalisia resessiivisiä 123, X- kromosomaalisia 17) geenivirheiden kantajuutta gnomAD-tietokannan aineistossa (v2.1) suomalaisessa (n= 12 500 henkilöä) sekä verrokkiväestöjen geeniperimässä. Geenit valittiin ACMG:n suositusten pohjalta sekä suomalaisen tautiperinnön geeneistä. gnomAD-aineistosta suodatettiin näiden geenien ClinVar-tietokannassa patogeeniseksi tai todennäköisesti patogeeniseksi luokitellut muutokset, suomalaiset valtamutaatiot ja loss-of-function muutokset., Näiden muutosten avulla arvioitiin kunkin geenin osalta yhteenlaskettu geenivirheiden kantajuus. Tulosten perusteella 47 geenin geenivirheiden kantajuus ylittää suosituksissa määritellyn 0,5 % rajan suomalaisväestössä. Autosomaalisten geenien osalta suomalaisväestössä kumulatiivinen kantajuusfrekvenssi on 51,1 % ja X- kromosomaalisten geenien osalta 0,5 %. Riskissä olevia pariskuntia on arviolta yhteensä vähintään 1,6 % väestöstä. Ne geenit, joiden geenivirheiden kantajuusfrekvenssi on yli 0,5 %, aiheuttavat 97,5 % kaikista perinnöllisesti sairaan lapsen saamisen riskissä olevista pariskunnista. Tulosten ja aiempien suositusten perusteella laajennettuun kantajuusseulontaan kannattaisi ottaa mukaan nämä 47 geeniä. Kaikkia geenivirheitä ei ole järkevää tai eettistä seuloa. Muun muassa vakavuuden määritelmä vaihtelee yhteisöittäin, ja siksi tämän tutkimuksen tulokset muodostavat vain alustavan pohjan laajennetulle kantajuusseulonnalle Suomessa.
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