Detección de la mutación de la enzima isocitrato deshidrogenasa en gliomas difusos grados II, III y IV / Detection of isocitrate dehydrogenase enzyme mutation in grades II, III and IV diffuse gliomas

Introducción. Los gliomas son las neoplasias malignas primarias más frecuentes del sistema nervioso central, asociadas con una mortalidad y morbilidad elevadas. Las mutaciones en los genes IDH1 e IDH2 de la enzima isocitrato deshidrogenasa (IDH) son clave en la tumorogénesis, y son consideradas un factor pronóstico importante en estas neoplasias. En este estudio se buscó determinar la presencia de mutaciones de los genes IDH1 e IDH2 en pacientes con diagnóstico de glioma difuso en diferentes grados, y su correlación con la sobrevida. Metodología. Se realizó un estudio descriptivo, prospectivo y retrospectivo. La población de estudio fueron pacientes entre los 18 y 45 años con diagnóstico de glioma difuso grado II, III y IV, atendidos en el Hospital San Vicente Fundación de Medellín, entre 2012 y 2017, en quienes se realizó un análisis de mutaciones en los genes IDH1 e IDH2 por secuenciación Sanger y tinción de inmunohistoquímica. Resultados. Se incluyeron 14 pacientes con edad promedio de 37 años, 57% de sexo masculino. Glioblastoma fue la neoplasia más frecuente, diagnosticada en el 42,9% de casos. Por inmunohistoquímica, 10 de los 14 (71,4%) pacientes presentaron mutación de la enzima IDH1, en tanto que 1 de los 11 (9%) pacientes en quienes se logró la secuenciación del gen IDH2, mostró mutación. En general, el 78,6% presentó mutaciones de la enzima IDH, con promedio de sobrevida de 48 meses. Conclusión. Estos hallazgos sugieren que los gliomas son un grupo heterogéneo de tumores, con gran variabilidad genética que impacta en su pronóstico y comportamiento

Introduction. Gliomas are the most common primary malignancies of the central nervous system, associated with high mortality and morbidity. Mutations in the isocitrate dehydrogenase (IDH) enzyme IDH1 and IDH2 genes, are key in tumorigenesis, and are considered an important prognostic factor in these neoplasms. This study aimed to determine the presence of IDH1 and IDH2 gene mutations in patients diagnosed with diffuse glioma in different degrees, and their correlation with survival. Methodology. A descriptive, prospective and retrospective study was conducted. The study population consisted of patients between the ages of 18 and 45 with a diagnosis of grade II, III and IV diffuse glioma, treated at the Hospital San Vicente Fundación in Medellín, between 2012 and 2017, in whom an analysis of IDH1 and IDH2 gene mutations was performed by Sanger sequencing and immunohistochemical staining. Results. Fourteen patients with a mean age of 37 years were included, 57% were male. Glioblastoma was the most frequent neoplasm, diagnosed in 42.9% of the cases. By immunohistochemistry, 10 of the 14 (71.4%) patients had a mutation of the IDH1 enzyme, while 1 of the 11 (9%) patients in whom IDH2 gene sequencing was achieved showed a mutation. In general, 78.6% had IDH enzyme mutations, with an average survival of 48 months. Conclusion. These findings suggest that gliomas are a heterogeneous group of tumors, withgreat genetic variability that impacts their prognosis and behavior

The mutational repertoire of uterine sarcomas and carcinosarcomas in a Brazilian cohort: A preliminary study

OBJECTIVES: The present study aimed to contribute to the catalog of genetic mutations involved in the carcinogenic processes of uterine sarcomas (USs) and carcinosarcomas (UCSs), which may assist in the accurate diagnosis of, and selection of treatment regimens for, these conditions. METHODS: We performed gene-targeted next-generation sequencing (NGS) of 409 cancer-related genes in 15 US (7 uterine leiomyosarcoma [ULMS], 7 endometrial stromal sarcoma [ESS], 1 adenosarcoma [ADS]), 5 UCS, and 3 uterine leiomyoma (ULM) samples. Quality, frequency, and functional filters were applied to select putative somatic variants. RESULTS: Among the 23 samples evaluated in this study, 42 loss-of-function (LOF) mutations and 111 missense mutations were detected, with a total of 153 mutations. Among them, 66 mutations were observed in the Catalogue of Somatic Mutations in Cancer (COSMIC) database. TP53 (48%), ATM (22%), and PIK3CA (17%) were the most frequently mutated genes. With respect to specific tumor subtypes, ESS showed mutations in the PDE4DIP, IGTA10, and DST genes, UCS exhibited mutations in ERBB4, and ULMS showed exclusive alterations in NOTCH2 and HER2. Mutations in the KMT2A gene were observed exclusively in ULM and ULMS. In silico pathway analyses demonstrated that many genes mutated in ULMS and ESS have functions associated with the cellular response to hypoxia and cellular response to peptide hormone stimulus. In UCS and ADS, genes with most alterations have functions associated with phosphatidylinositol kinase activity and glycerophospholipid metabolic process. CONCLUSION: This preliminary study observed pathogenic mutations in US and UCS samples. Further studies with a larger cohort and functional analyses will foster the development of a precision medicine-based approach for the treatment of US and UCS.

Molecular characterization and subtyping of Blastocystis in urticarial patients in Turkey

Objective: To investigate Blastocystis' etiologic role and association with gastrointestinal symptomatology in acute and chronic urticaria patients and to identify Blastocystis subtypes responsible for urticaria. Methods: The study included urticaria patients and healthy individuals that presented to our polyclinic between June 2015 and May 2017. The participants were assigned into Group I (137 patients), subdivided into acute (72) and chronic urticaria patients (65), and Group ? (129 control individuals). Blastocystis presence was investigated by native-Lugol examination, trichrome staining, PCR using sequence tagged site primers, and DNA sequencing analysis. The phylogenetic tree was constructed. Results: The native-Lugol and trichrome staining methods revealed that 16 patients (16/133, 12.0%) had Blastocystis-positive stool samples, of which seven samples (7/133, 5.3%) belonged acute and nine (9/133, 6.8%) to chronic urticaria patients. Concerning Blastocystis subtypes, of the acute urticaria patients, three had subtype 1 (ST1), one had ST2, and three had ST3. Of the chronic urticaria patients, one had ST1 and eight had ST3. Blastocystis positivity was detected in two control individuals (2/123, 1.6%), both being ST3. All subtypes identified by PCR were confirmed by the sequencing analysis. The acute and chronic urticaria groups showed no statistically significant differences for Blastocystis positivity (P=0.60) and subtype distribution (P=0.15). A statistically significant difference was found between the urticaria patients and the controls for Blastocystis positivity (P<0.01), but not for subtype distribution (P=0.67) or for Blastocystis presence and gastrointestinal complaints. Conclusions: This study on Blastocystis subtype distribution among Turkish urticaria patients showed results consistent with the literature. It was concluded that Blastocystis should be kept in mind in patients with urticaria.

Statistical Analysis of Metagenomics Data

Understanding the role of the microbiome in human health and how it can be modulated is becoming increasingly relevant for preventive medicine and for the medical management of chronic diseases. The development of high-throughput sequencing technologies has boosted microbiome research through the study of microbial genomes and allowing a more precise quantification of microbiome abundances and function. Microbiome data analysis is challenging because it involves high-dimensional structured multivariate sparse data and because of its compositional nature. In this review we outline some of the procedures that are most commonly used for microbiome analysis and that are implemented in R packages. We place particular emphasis on the compositional structure of microbiome data. We describe the principles of compositional data analysis and distinguish between standard methods and those that fit into compositional data analysis.

Identification of Candida Species Using 26S Ribosomal RNA Gene Sequencing in Patients with Periodontitis

The infection with Candida spp. for oral cavity is being increasingly reported. However, its variations have not yet been specifically described in periodontitis. The present study was conducted to use an uniplex 26S rRNA-based amplicons to detect and discriminate Candida using only one pair of ribosomal primers. A total of 50 patients with chronic periodontitis was involved in the study. Pure Candida colonies were isolated from 23 patients and genomic DNA was extracted, and PCR was conducted. Direct DNA sequencing followed by comprehensive phylogenetic analyses were performed to confirm the identity of Candida colonies. Results indicated that the ration of Candida-infected patients was 46%, with a high prevalence of C. albicans, followed by remarkably lower ratios of C. parapsilosis, C. glabrata, C. kefyr, and C. dubliniensis respectively. Phylogenetic analyses indicated obvious discrimination amongst the analyzed Candida species as each observed species occupied a distinctive phylogenetic position. The current results reported a simple, efficient, and low-cost detection of five species of Candida without the need for other costly techniques of molecular screening. The current findings may help dentists to easily take a snapshot of the patterns of Candida infection in periodontitis cases to assess the nature and grade of infection.

Molecular characterization and subtyping of Blastocystis in urticarial patients in Turkey

Objective: To investigate Blastocystis' etiologic role and association with gastrointestinal symptomatology in acute and chronic urticaria patients and to identify Blastocystis subtypes responsible for urticaria. Methods: The study included urticaria patients and healthy individuals that presented to our polyclinic between June 2015 and May 2017. The participants were assigned into Group I (137 patients), subdivided into acute (72) and chronic urticaria patients (65), and Group ? (129 control individuals). Blastocystis presence was investigated by native-Lugol examination, trichrome staining, PCR using sequence tagged site primers, and DNA sequencing analysis. The phylogenetic tree was constructed. Results: The native-Lugol and trichrome staining methods revealed that 16 patients (16/133, 12.0%) had Blastocystis-positive stool samples, of which seven samples (7/133, 5.3%) belonged acute and nine (9/133, 6.8%) to chronic urticaria patients. Concerning Blastocystis subtypes, of the acute urticaria patients, three had subtype 1 (ST1), one had ST2, and three had ST3. Of the chronic urticaria patients, one had ST1 and eight had ST3. Blastocystis positivity was detected in two control individuals (2/123, 1.6%), both being ST3. All subtypes identified by PCR were confirmed by the sequencing analysis. The acute and chronic urticaria groups showed no statistically significant differences for Blastocystis positivity (P=0.60) and subtype distribution (P=0.15). A statistically significant difference was found between the urticaria patients and the controls for Blastocystis positivity (P<0.01), but not for subtype distribution (P=0.67) or for Blastocystis presence and gastrointestinal complaints. Conclusions: This study on Blastocystis subtype distribution among Turkish urticaria patients showed results consistent with the literature. It was concluded that Blastocystis should be kept in mind in patients with urticaria.

First identified Korean family with Tatton-Brown-Rahman Syndrome caused by the novel DNMT3A variant c.118G>C p.(Glu40Gln)

Tatton-Brown-Rahman Syndrome (TBRS), an overgrowth syndrome caused by heterozygous mutation of DNMT3A, first was described in 2014. Approximately 60 DNMT3A variants, including 32 missense variants, have been reported, with most missense mutations located on the DNMT3A functional domains. Autosomal dominant inheritance by germ-line mutation of DNMT3A has been reported, but vertical transmission within a family is extremely rare. Herein, we report the first Korean family with maternally inherited TBRS due to the novel heterozygous DNMT3A variant c.118G>C p.(Glu40Gln), located outside the main functional domain and identified by multigene panel sequencing. The patient and her mother had typical clinical features, including tall stature during childhood, macrocephaly, intellectual disability, and characteristic facial appearance. TBRS shows milder dysmorphic features than other overgrowth syndromes, potentially leading to underdiagnosis and underestimated prevalence; thus, targeted multigene panel sequencing including DNMT3A will be a useful tool in cases of overgrowth and unexplained mild intellectual disability for early diagnosis and genetic counseling.

Sequencing analysis of HPV-other type on an HPV DNA chip

OBJECTIVES: To identify the specific human papillomavirus (HPV) genotypes from HPV-other type on an HPV DNA chip test by sequencing. METHODS: Among 13,600 women undergoing a routine gynecology examination including Pap smear and/or HPV test by DNA chip test in the healthcare system at Gangnam Center from July 2012 to February 2013, we prospectively collected and performed sequencing for a total of 351 consecutive cervicovaginal samples consisting of 180 samples that tested positive for HPV-other type and 171 samples that tested positive for either high-risk HPV or low-risk HPV. RESULTS: Of a total of 351 samples, individual HPV genotypes were successfully sequenced in 215 cases: 119 HPV-other type, 82 HPV-high-risk, and 14 HPV-low-risk. Based on the sequencing for 119 HPV-other type samples, 91.6% were detected as HPV types that were not included on the DNA chip; however, 7.6% (9/119) were proven to be high-risk HPV types: HPV 18 (n=4), HPV 33 (n=3), HPV 35 (n=1), and HPV 59 (n=1). For correlation analysis of all high-risk and HPV 16/18, the correlation rate was 76.2% and 86.6% with kappa-value of 0.38 and 0.69, respectively. CONCLUSION: HPV-other type on DNA chip test may still have possibility of high-risk HPV, i.e., HPV 18 and thus the significance of HPV-other type in detecting cervical disease remains to be investigated.

Detection of Innate and Artificial Mitochondrial DNA Heteroplasmy by Massively Parallel Sequencing: Considerations for Analysis

BACKGROUND: Mitochondrial heteroplasmy, the co-existence of different mitochondrial polymorphisms within an individual, has various forensic and clinical implications. But there is still no guideline on the application of massively parallel sequencing (MPS) in heteroplasmy detection. We present here some critical issues that should be considered in heteroplasmy studies using MPS. METHODS: Among five samples with known innate heteroplasmies, two pairs of mixture were generated for artificial heteroplasmies with target minor allele frequencies (MAFs) ranging from 50% to 1%. Each sample was amplified by two-amplicon method and sequenced by Ion Torrent system. The outcomes of two different analysis tools, Torrent Suite Variant Caller (TVC) and mtDNA-Server (mDS), were compared. RESULTS: All the innate heteroplasmies were detected correctly by both analysis tools. Average MAFs of artificial heteroplasmies correlated well to the target values. The detection rates were almost 90% for high-level heteroplasmies, but decreased for low-level heteroplasmies. TVC generally showed lower detection rates than mDS, which seems to be due to their own computation algorithms which drop out some reference-dominant heteroplasmies. Meanwhile, mDS reported several unintended low-level heteroplasmies which were suggested as nuclear mitochondrial DNA sequences. The average coverage depth of each sample placed on the same chip showed considerable variation. The increase of coverage depth had no effect on the detection rates. CONCLUSION: In addition to the general accuracy of the MPS application on detecting heteroplasmy, our study indicates that the understanding of the nature of mitochondrial DNA and analysis algorithm would be crucial for appropriate interpretation of MPS results.

Correlation between molecular features and genetic subtypes of Glioblastoma: critical analysis in 109 cases / Correlação entre as características moleculares e os subtipos genéticos dos glioblastomas: análise crítica de 109 casos

OBJECTIVE: Glioblastoma, the most common and lethal brain tumor, is also one of the most defying forms of malignancies in terms of treatment. Integrated genomic analysis has searched deeper into the molecular architecture of GBM, revealing a new sub-classification and promising precision in the care for patients with specific alterations. METHOD: Here, we present the classification of a Brazilian glioblastoma cohort into its main molecular subtypes. Using a high-throughput DNA sequencing procedure, we have classified this cohort into proneural, classical and mesenchymal sub-types. Next, we tested the possible use of the overexpression of the EGFR and CHI3L1 genes, detected through immunohistochemistry, for the identification of the classical and mesenchymal subtypes, respectively. RESULTS: Our results demonstrate that genetic identification of the glioblastoma subtypes is not possible using single targeted mutations alone, particularly in the case of the Mesenchymal subtype. We also show that it is not possible to single out the mesenchymal cases through CHI3L1 expression. CONCLUSION: Our data indicate that the Mesenchymal subtype, the most malignant of the glioblastomas, needs further and more thorough research to be ensure adequate identification.

OBJETIVO: O glioblastoma (GBM), o tumor cerebral mais comum e mais letal, é também um dos tipos de tumores de mais difícil tratamento. Análises genômicas integradas têm contribuído para um melhor entendimento da arquitetura molecular dos GBMs, revelando uma nova subclassificação com a promessa de precisão no tratamento de pacientes com alterações específicas. Neste estudo, nós apresentamos a classificação de uma casuística brasileira de GBMs dentro dos principais subtipos do tumor. MÉTODO: Usando sequenciamento de DNA em larga escala, foi possível classificar os tumores em proneural, clássico e mesenquimal. Em seguida, testamos o possível uso da hiperexpressão de EGFR e CHI3L1 para a identificação dos subtipos clássico e mesenquimal, respectivamente. RESULTADOS: Nossos resultados deixam claro que a identificação genética dos subtipos moleculares de GBM não é possível utilizando-se apenas um único tipo de mutação, em particular nos casos de GBMs mesenquimais. Da mesma forma, não é possível distinguir os casos mesenquimais apenas com a expressão de CHI3L1. CONCLUSÃO: Nossos dados indicam que o subtipo mesenquimal, o mais maligno dos GBMs, necessita de uma análise mais aprofundada para sua identificação.

Mutational spectrum in breast cancer associated BRCA1 and BRCA2 genes in Colombia / Espectro de mutaciones en los genes BRCA1 y BRCA2 asociados a cáncer de mama en Colombia

Abstract Introduction: The risk of developing breast and ovarian cancer is higher in families that carry mutations in BRCA1 or BRCA2 genes, and timely mutation detection is critical. Objective: To identify the presence of mutations in the Colombian population and evaluate two testing strategies. Methods: From a total universe of 853 individual blood samples referred for BRCA1 and BRCA2 typing, 256 cases were analyzed by complete direct sequencing of both genes in Myriad Genetics, and the remaining 597 cases were studied by partial sequencing based on founder mutations in a PCR test designed by ourselves ("Profile Colombia"). Results: We found 107 patients carrying deleterious mutations in this group of patients, 69 (64.5%) located in BRCA1, and 38 (35.5%) in BRCA2. Overall, we detected 39 previously unreported mutations in Colombia (22 in BRCA1 and 17 in BRCA2) and only 4 out of the 6 previously reported founder mutations. Sixty four out of 597 patients (10.7%) studied by "Profile Colombia" showed mutations in BRCA1 or BRCA2, and 41/256 patients (16%) showed mutations by complete BRCA1-BRCA2 sequencing. Conclusions: The spectrum of 44 different mutations in Colombia as detected in our study is broader than the one previously reported for this country. "Profile Colombia" is a useful screening test to establish both founder and new mutations (detection rate of 10.7%) in cases with family history of breast cancer. Complete sequencing shows a detection rate of 16.0%, and should complement the study of the genetic basis of this disease.

Resumen Introducción: El riesgo de desarrollar cáncer de mama y cáncer de ovario puede transmitirse en familias que porten mutaciones en los genes BRCA1 o BRCA2. La detección de estas mutaciones permite tomar decisiones oportunas en el ámbito de la medicina preventiva. Objetivo: Estudiar el espectro de mutaciones en la población colombiana y evaluar dos estrategias de detección. Metodos: Se incluyeron en total 853 pacientes con diagnóstico de cáncer de mama y con solicitud de análisis de los genes BRCA1 y BRCA2. Un total de 256 pruebas se analizaron mediante secuencia directa completa de estos genes en Myriad Genetics, y las restantes 597 se estudiaron mediante secuencia parcial basada en mutaciones fundadoras a través de la prueba "Perfil Colombia", implementada por nosotros. Resultados: Se detectaron 107 pacientes portadores de mutaciones en pacientes colombianos, 69 de las cuales estaban localizadas en BRCA1 y 38 en BRCA2. De estas 39 mutaciones son nuevas (22 en BRCA1 y 17 en BRCA2) y solo se hallaron 4 de las 6 mutaciones reportadas previamente como fundadoras en Colombia. En 64/597 pacientes analizados mediante el "Perfil Colombia" se detectaron mutaciones en BRCA1 o BRCA2, así como en 41/256 pacientes que solicitaron la secuenciación completa de los genes BRCA1 y BRCA2. Conclusiones: El espectro de mutaciones fundadoras en Colombia es más amplio que el reportado anteriormente para este país. El "Perfil Colombia" es una prueba que revela a la vez mutaciones fundadoras y mutaciones nuevas, con una tasa de detección del 10.7%. La secuenciación completa presenta una tasa de detección del 16.0% y puede complementar el diagnóstico de la base genética de esta enfermedad.

Double primary lung adenocarcinoma diagnosed by epidermal growth factor receptor mutation status / 영남의대학술지

A nodular density was detected on a chest radiograph taken from a 57-year-old Korean woman who was visiting a hospital for a routine check. Chest computed tomography revealed a 4.8 cm lobulated mass in the right lung and another focal nodular lesion in the left lung; biopsies of both lungs revealed adenocarcinoma. We conducted DNA sequencing and peptide nucleic acid clamping to investigate the potential double primary lung cancer. The results verified that the mass in the right lung had a mutation in the epidermal growth factor receptor, whereas the nodule in the left lung had a wild-type sequence, showing that these two were genetically different cancers from one another. Thus, we demonstrate that genetic testing is useful in determining double primary lung cancer, and we herein report on this case.

Application of next-generation sequencing in research and personalized treatment of glioma / 第二军医大学学报

Glioma is a highly lethal malignancy and multiple challenges remain for it in the genomic study and clinical treatment. Next-generation sequencing (NGS) holds many advantages, and NGS can comprehensively analyze the whole genome, exome, transcriptome and epigenome to deepen the understanding of tumor genomics; and now, it has been successfully applied in the clinical study of some tumors, especially in personalized treatment for these tumors. At present, NGS has also been a hot in glioma research to clarify the pathogenesis of glioma, so as to draw up a personalized treatment method to benefit the patients.

Application of next-generation sequencing in research and personalized treatment of glioma / 第二军医大学学报

Glioma is a highly lethal malignancy and multiple challenges remain for it in the genomic study and clinical treatment.Next-generation sequencing (NGS) holds many advantages,and NGS can comprehensively analyze the whole genome,exome,transcriptome and epigenome to deepen the understanding of tumor genomics;and now,it has been successfully applied in the clinical study of some tumors,especially in personalized treatment for these tumors.At present,NGS has also been a hot in glioma research to clarify the pathogenesis of glioma,so as to draw up a personalized treatment method to benefit the patients.

Double primary lung adenocarcinoma diagnosed by epidermal growth factor receptor mutation status / 영남의대학술지

A nodular density was detected on a chest radiograph taken from a 57-year-old Korean woman who was visiting a hospital for a routine check. Chest computed tomography revealed a 4.8 cm lobulated mass in the right lung and another focal nodular lesion in the left lung; biopsies of both lungs revealed adenocarcinoma. We conducted DNA sequencing and peptide nucleic acid clamping to investigate the potential double primary lung cancer. The results verified that the mass in the right lung had a mutation in the epidermal growth factor receptor, whereas the nodule in the left lung had a wild-type sequence, showing that these two were genetically different cancers from one another. Thus, we demonstrate that genetic testing is useful in determining double primary lung cancer, and we herein report on this case.

Prenatal screening for Down's syndrome: Recent progress / 第二军医大学学报

Down's syndrome is an autosomal disease and its prenatal screening is particularly important. In recent years, clinical application of serological screening markers has been widely used, which improved the detection rate of Down's syndrome, but still remained at about 60%. The new generation of sequencing technology for direct analysis of nucleic acids, which can be used for fetal chromosomal aneuploidy detection, can detect Down's syndrome more accurately. In this paper, we compared the prenatal screening methods for Down's syndrome in recent decades, and reviewed the new screening markers based on proteomics and bioinformatics technology for clinical application.

Comparative analyses of classical phenotypic method and ribosomal RNA gene sequencing for identification of medically relevant Candida species

As the distribution of Candida species and their susceptibility to antifungal agents have changed, a new means of accurately and rapidly identifying these species is necessary for the successful early resolution of infection and the subsequent reduction of morbidity and mortality. The current work aimed to evaluate ribosomal RNA gene sequencing for the identification of medically relevant Candida species in comparison with a standard phenotypic method. Eighteen reference strains (RSs), 69 phenotypically identified isolates and 20 inconclusively identified isolates were examined. Internal transcribed spaces (ITSs) and D1/D2 of the 26S ribosomal RNA gene regions were used as targets for sequencing. Additionally, the sequences of the ITS regions were used to establish evolutionary relationships. The sequencing of the ITS regions was successful for 88% (94/107) of the RS and isolates, whereas 100% of the remaining 12% (13/107) of the samples were successfully analysed by sequencing the D1/D2 region. Similarly, genotypic analysis identified all of the RS and isolates, including the 20 isolates that were not phenotypically identified. Phenotypic analysis, however, misidentified 10% (7/69) of the isolates. Phylogenetic analysis allowed the confirmation of the relationships between evolutionarily close species. Currently, the use of genotypic methods is necessary for the correct identification of Candida species.

Annotation of Genes Having Candidate Somatic Mutations in Acute Myeloid Leukemia with Whole-Exome Sequencing Using Concept Lattice Analysis

In cancer genome studies, the annotation of newly detected oncogene/tumor suppressor gene candidates is a challenging process. We propose using concept lattice analysis for the annotation and interpretation of genes having candidate somatic mutations in whole-exome sequencing in acute myeloid leukemia (AML). We selected 45 highly mutated genes with whole-exome sequencing in 10 normal matched samples of the AML-M2 subtype. To evaluate these genes, we performed concept lattice analysis and annotated these genes with existing knowledge databases.

Genetic Risk Prediction for Normal-Karyotype Acute Myeloid Leukemia Using Whole-Exome Sequencing

Normal-karyotype acute myeloid leukemia (NK-AML) is a highly malignant and cytogenetically heterogeneous hematologic cancer. We searched for somatic mutations from 10 pairs of tumor and normal cells by using a highly efficient and reliable analysis workflow for whole-exome sequencing data and performed association tests between the NK-AML and somatic mutations. We identified 21 nonsynonymous single nucleotide variants (SNVs) located in a coding region of 18 genes. Among them, the SNVs of three leukemia-related genes (MUC4, CNTNAP2, and GNAS) reported in previous studies were replicated in this study. We conducted stepwise genetic risk score (GRS) models composed of the NK-AML susceptible variants and evaluated the prediction accuracy of each GRS model by computing the area under the receiver operating characteristic curve (AUC). The GRS model that was composed of five SNVs (rs75156964, rs56213454, rs6604516, rs10888338, and rs2443878) showed 100% prediction accuracy, and the combined effect of the three reported genes was validated in the current study (AUC, 0.98; 95% confidence interval, 0.92 to 1.00). Further study with large sample sizes is warranted to validate the combined effect of these somatic point mutations, and the discovery of novel markers may provide an opportunity to develop novel diagnostic and therapeutic targets for NK-AML.

AnsNGS: An Annotation System to Sequence Variations of Next Generation Sequencing Data for Disease-Related Phenotypes / 대한의료정보학회지

OBJECTIVES: Next-generation sequencing (NGS) data in the identification of disease-causing genes provides a promising opportunity in the diagnosis of disease. Beyond the previous efforts for NGS data alignment, variant detection, and visualization, developing a comprehensive annotation system supported by multiple layers of disease phenotype-related databases is essential for deciphering the human genome. To satisfy the impending need to decipher the human genome, it is essential to develop a comprehensive annotation system supported by multiple layers of disease phenotype-related databases. METHODS: AnsNGS (Annotation system of sequence variations for next-generation sequencing data) is a tool for contextualizing variants related to diseases and examining their functional consequences. The AnsNGS integrates a variety of annotation databases to attain multiple levels of annotation. RESULTS: The AnsNGS assigns biological functions to variants, and provides gene (or disease)-centric queries for finding disease-causing variants. The AnsNGS also connects those genes harbouring variants and the corresponding expression probes for downstream analysis using expression microarrays. Here, we demonstrate its ability to identify disease-related variants in the human genome. CONCLUSIONS: The AnsNGS can give a key insight into which of these variants is already known to be involved in a disease-related phenotype or located in or near a known regulatory site. The AnsNGS is available free of charge to academic users and can be obtained from http://snubi.org/software/AnsNGS/.