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PubMed1995

[Variants of psychosomatic personality development in diseases of the gastrointestinal tract].

612 patients with different psychosomatic disorders of gastrointestinal tract (GIT) were examined. They included either 200 patients with organic stomach disease or with duodenal ulcer as well as 412 individuals with various functional disorders of GIT such as psychogenic vomiting, dysphagia, gastralgia and colon irritability syndrome. In 70% of all cases patientc relatives (1-3 degree of relationship) had also some psychosomatic diseases. All the patients suffered in childhood from so-called GIT-variant of children's neuropathia. Being adults they all met intensive or moderate stress and developed psychogenic depression. Two ways of psychosomatic disorders cristallization on the background of depression were observed, exactly reactivation of children's neuropathia symptomes or rapid affect somatization which were followed by psychosomatic cycles formation and by stress tolerance decrease. Several types of psychosomatic development were described: hypochondrial (78.8%), asthenic (12.4%), obsessive (2.3%), hysterical (4.4%) and paranoial (2.1%).

Adult↗

PubMed2026

Clinical Variant Interpretation with the Integrative Genomics Viewer (IGV) for Molecular Pathologists.

The integrative genomics viewer (IGV) is a pivotal tool in clinical genomics, enabling the visualization and interpretation of complex sequencing data. Bringing clinical knowledge to bear with visual evaluation of sequencing results is the primary means by which molecular pathologists and other professionals assess and finalize cases. A variety of software tools can assist, but their relationship to the underlying data must be understood and applied systematically. This study includes essential background on next-generation sequencing (NGS) data file types (e.g., FASTQ, BAM, VCF) with a discussion of their format and purpose. We then describe features of IGV that derive nuances from these files. We utilize a series of curated practical cases based on clinical vignettes through which the reader will interact with clinical NGS sequencing data using the IGV software to review various types of clinically relevant variants relative to the human reference genome. These clinical vignettes have been curated to describe examples of some of the complexities of interpretation of genomic data, and how utilizing IGV as part of a routine workflow can provide additional interpretive information for variants beyond routine bioinformatic software algorithm variant calls. The visual inspection of genomic variants utilizing the tools within IGV can unmask subtle contextual cues (i.e., variant allele frequency, strand bias, tissue-specific context) that can influence the interpretation of genomic variants. Although this study focuses on using IGV for the detection and interpretation of somatic variants, the provided applications can be extrapolated for use in the germline setting, including analysis of complex variants and detection of mosaicism.

Humans↗

PubMed2005

Developmental stage-selective effect of somatically mutated leukemogenic transcription factor GATA1.

Acquired mutations in the hematopoietic transcription factor GATA binding protein-1 (GATA1) are found in megakaryoblasts from nearly all individuals with Down syndrome with transient myeloproliferative disorder (TMD, also called transient leukemia) and the related acute megakaryoblastic leukemia (DS-AMKL, also called DS-AML M7). These mutations lead to production of a variant GATA1 protein (GATA1s) that is truncated at its N terminus. To understand the biological properties of GATA1s and its relation to DS-AMKL and TMD, we used gene targeting to generate Gata1 alleles that express GATA1s in mice. We show that the dominant action of GATA1s leads to hyperproliferation of a unique, previously unrecognized yolk sac and fetal liver progenitor, which we propose accounts for the transient nature of TMD and the restriction of DS-AMKL to infants. Our observations raise the possibility that the target cells in other leukemias of infancy and early childhood are distinct from those in adult leukemias and underscore the interplay between specific oncoproteins and potential target cells.

Adult↗

PubMed2026

Genomic Characterization of ETV6::RUNX1-Positive Childhood B-ALL in a Chinese Cohort: Novel Fusion Partners, Co-Occurring Mutations, and Risk-Stratifying Biomarkers.

BACKGROUND: ETV6::RUNX1 is the most common genetic abnormality in pediatric B-cell acute lymphoblastic leukemia (ALL; ∼25%), yet the comprehensive genetic architecture and molecular predictors of intermediate-risk (IR) stratification remain incompletely characterized. METHODS: We performed whole-transcriptome sequencing (Illumina NovaSeq 6000, rRNA depletion, 41.70 Gb/sample) on bone marrow samples from 93 pediatric ETV6::RUNX1-positive B-ALL patients. Bioinformatics analysis included STAR alignment, MuTect2 variant calling, FusionCatcher fusion detection, and VEP annotation. The Jaccard index with permutation testing assessed mutation co-occurrence; logistic regression identified independent predictors of IR classification. RESULTS: Beyond ETV6::RUNX1, we identified 51 distinct fusion genes across the cohort, including the reciprocal RUNX1-ETV6 (73.1%), chr8::KLF1210 (38.7%), and KLF12-chr8 (34.4%). Somatic mutations in 249 genes were detected; the most frequent were KIAA1715 (17.2%), KRAS (11.8%), and NSD2 (10.8%). Network analysis revealed significant chromatin modifier co-occurrence (KIAA1715-KMT2C: J = 0.136, p = 0.015) and KRAS-NRAS mutual exclusivity (J = 0.000, p = 0.042). PTCH1 (OR = 3.50, 95% CI 0.21-58.49, p = 0.41) and GNB1 (OR = 6.5, 95% CI 1.2-34.8, p = 0.029) mutations independently predicted IR classification. chr8::KLF1210 fusion correlated with higher Day-19 MRD levels (p = 0.038). CONCLUSIONS: GNB1 mutation represents a novel independent predictor of IR stratification in ETV6::RUNX1-positive B-ALL. The chromatin modifier co-occurrence module and extensive fusion architecture reveal biological heterogeneity within this favorable-risk subtype, with potential implications for risk-adapted therapeutic strategies.

B‐ALL↗

PubMed1989

Induction of tumor-cell lysis by bi-specific monoclonal antibodies recognizing renal-cell carcinoma and CD3 antigen.

Bi-specific monoclonal antibodies (MAbs) were developed by somatic hybridization of 2 mouse hybridomas, one producing MAb against the G250 renal-cell carcinoma (RCC)-associated antigen and the other against the T-cell antigen CD3 (OKT3). The dual specificity of the hybrid MAb produced by these so-called quadromas was analyzed by immunohistochemistry on tissue sections and by cytotoxicity assays with relevant target and effector cells. The bi-specific MAb could induce TCR alpha beta/CD3+ and TCR gamma delta/CD3+ cloned lymphocytes to kill RCC cells. A noteworthy finding was that the TCR alpha beta and gamma delta lymphocyte clones showed different triggering abilities. The specificity of target-cell lysis by the cytotoxic T cells (CTL) was dictated by the specificity of the G250 MAb. Control bi-specific MAb, recognizing a cell-surface structure not involved in T-cell activation, did not induce lysis. Several IgG subclass switch variants of the G250 hybridoma, i.e., IgG1, 2a, 2b and IgE, were used for somatic hybridization with the OKT3 hybridoma (IgG2a). Except for IgE, all IgG subclass combinations could equally induce cytolysis. Induction of cytolysis was inhibited only by excess OKT3 MAb. Comparison of 2 bi-specific MAb preparations of the same combination (IgG2a/1), produced by 2 quadromas derived from the same parental hybridomas after identical purification procedures, produced different amounts of bispecific MAb.

Animals↗

PubMed2000

Sequence conservation and expression of the sex-lethal homologue in the fly Megaselia scalaris.

Sex-lethal (Sxl) is Drosophila melanogaster's key regulating gene in the sex-determining cascade. Its homologue in Megaselia scalaris, the chromosome 3 gene Megsxl, codes for a protein with an overall similarity of 77% with the corresponding D. melanogaster sequence. Expression in M. scalaris, however, is very unlike that in D. melanogaster. Megsxl transcripts with a long ORF occur in both sexes. Differential splicing is conserved but not sex-specific. There are several splice variants, among them one is common to gonads and somatic tissues of all developmental stages investigated, one is specific for ovaries and embryos, and a third one is not found in ovaries. In the ovary, Megsxl is heavily transcribed in nurse cells and transported into eggs. These results suggest a non-sex-determining function during early embryogenesis; the presence of Megsxl RNA in testes and somatic tissues calls for other (or more) functions.

Age Factors↗

PubMed2002

[WHO classification of testicular tumors].

Twenty years after the first edition (1977), the WHO has presented the updated version of the "Histological typing of testis tumours". The revised classification was necessary because some clinically important new entities have been described in recent years. The most important is obviously the precursor lesion of germ cell tumors, which has been called "intratubular malignant germ cells". Such atypical cells appear in the tubules adjacent to the germ cell tumors, in some few cases (6%) also in the contra lateral healthy gonad and rarely in infertile men (1%). The precursor lesion can progress to franc germ cell tumor starting probably with seminoma, which still maintain the capability of differentiation (pluripotente cells) in all other types of non-seminomatous germ cell tumors. This lesion is missed in germ cell tumors of childhood and in spermatocytic seminomas, both seem to have a histogenetic history rather different from the other germ cell in adults. The categories used in the first classification have been preserved and some new diagnoses added. Most of the new diagnoses are subtypes--called "variants"--of well known tumors. Seminoma with syncytiotrophoblastic cells is a variant which should not be confused with choriocarcinoma. Spermatocytic seminomas are perfectly benign tumors but they become a life threatening disease when combined with sarcomas (new entity). In the group of mature teratomas the "dermoid cyst" appears as a benign subtype mostly observed in children. Unfortunately, however, the old term "teratoma with malignant transformation" was changed to "teratoma with malignant areas" in the 1998 classification. This is a harmless name for an extremely dangerous tumor in which one tissue overgrows the other and gives rise to somatic type sarcomas or carcinomas. Such tumors do not respond like germ cell tumors to the usual chemotherapy. Treatment should be tailored according to that used in standard management of the respective sarcoma or carcinoma. In the comments it is mentioned that the testis carcinoid could be a part of teratoma, but the diagnosis is listed in the group of "miscellaneous" tumors together with tumors of ovarian epithelial type. This is a very questionable decision because the normal testis does not contain neuroendocrine cells from which carcinoids would have to be able to develop. Teratomas, however, show plenty of them producing all kinds of typical hormones. "Large cell calcifying Sertoli cell tumour" has been recently described and can be sporadic or inherited. This morphologically peculiar tumor can be part of the Swiss syndrome also called Carney's complex. The patients have cardiac myxomas, spotty skin pigmentation, hormone active nodular hyperplasia of the adrenals and soft tissue myxomas. The newly appearing "mixed germ cell--sex cord/gonadal stromal tumours, unclassified" has a histology similar to the well known gonadoblastomas. In contrast to gonadoblastoma, however, these tumors occur in testes of genotypic and phenotypic normal males. From the practical, diagnostic point of view the new classification does not contain dramatic changes. For the therapy of germ cell tumor an assessment of risk factors found by the pathologists is extremely important. The most important independent predictors of relapse are tumor invasion of blood or lymph-vessels, absence of yolk sac elements and the presence of an embryonal carcinoma component. In the absence of such predictors a surveillance policy allows some patients to forgo chemotherapy.

Humans↗

PubMed2026

Strategies for mosaic variant calling in brain disorders.

The human brain is a genomic mosaic, where postzygotic mutations arising from embryogenesis to senescence drive diverse neurodevelopmental and neurodegenerative diseases. Because of numerous sequencing artifacts at ultralow variant allele frequencies (VAFs), detecting these variants remains a significant analytical challenge. This review focuses on single-nucleotide variants and small indels, summarizing current strategies for aligning sampling methods, including bulk, laser capture microdissection, and single-cell genomics, with the expected clonal architecture of the brain. It emphasizes that mosaic detection sensitivity is fundamentally constrained by sequencing depth, since even the most advanced algorithms cannot identify variants not physically represented in the sequencing library. The review further recommends the selection of variant calling algorithms based on validated VAF detection performance, matching tools like MuTect2 and MosaicForecast to their optimal performance ranges. Furthermore, we discuss how multitissue sampling, as emphasized by the SMaHT project, addresses the matched-control dilemma and supports accurate variant classification via cross-tissue VAF gradients. Integrating these established pipelines with multiomics modalities, including transcriptomic and epigenetic data, could advance the field toward a functional understanding of how the somatic genome impacts human brain health and disease.

Humans↗

PubMed1981

Genetic variation for prolidase (PEP-4) in the mouse maps near the gene for glucosephosphate isomerase (GPI-1) on chromosome 7.

An inherited electrophoretic variant of prolidase (EC 3.4.13.9), also called peptidase 4 (PEP-4), has been discovered among inbred strains of mice. Analysis of progeny from reciprocal backcrosses established that the electrophoretic forms are expressed codominantly and that Pep-4 is located between the genes for glucosephosphate isomerase (Gpi-1) and pink-eyed dilution (p) on chromosome 7. These data define a region of conserved gene linkage between mouse chromosome 7 and human chromosome 19, as originally indicated by somatic cell hybrid studies, and imply that human prolidase (PEPD) is located in the region of human chromosome 19 pter greater than q13.

Animals↗

PubMed2026

Molecular residual disease assessment in colorectal and bladder cancer by somatic structural variant analysis of cell-free DNA whole-genome sequencing data.

BACKGROUND: Whole-genome sequencing (WGS)-based methods for circulating tumor DNA (ctDNA) detection typically rely on tumor-informed identification of somatic single nucleotide variants (SNVs). Somatic structural variants (SVs) are another type of cancer-specific genomic alteration, which owing to their larger genomic footprint and unique breakpoint junctions, are easier to distinguish from sequencing noise than SNVs. They are, however, rarely used for ctDNA detection because of (1) artifacts from WGS procedures that SV callers may falsely interpret as genuine SVs. This makes it difficult to establish high-confidence SV catalogos from short-read tumor WGS and can cause false-positive ctDNA detections. (2) Lack of robust strategies to quantify SV-supporting reads in plasma WGS. To address these barriers and enable integration of SV biomarkers into WGS-based ctDNA detection, we present a bioinformatic framework for algorithmic curation of somatic SV calls from fresh-frozen and formalin-fixed paraffin-embedded (FFPE) tumors, coupled with a novel approach for sensitive, accurate mapping and quantification of SV breakpoint-supporting reads in plasma WGS. METHODS: Tumor, normal and plasma WGS data from 144 patients with stage III colorectal cancer was used to establish the bioinformatic framework. This included ~30x WGS data from 1564 serially collected plasma samples. The framework was validated using tumor/normal/plasma WGS data from 32 patients with muscle-invasive bladder cancer. SV-based ctDNA detection was benchmarked against previously published SNV-based ctDNA results for the same samples. RESULTS: After curation of SV calls and quantification in plasma WGS, our SV-based approach enabled robust ctDNA detection with overall specificity exceeding 99% in plasma samples. Furthermore, we observed strong concordance (Pearson’s r > 0.93, p < 2.2 × 10− 16) between ctDNA-positive samples identified by our SV-based method and previous SNV-based analyses, validating the reliability of our approach. Finally, we demonstrated application of the method in an independent bladder cancer cohort, highlighting its generalizability and potential clinical use. CONCLUSIONS: We provide a bioinformatic framework that establishes somatic SVs as ultra-specific biomarkers for WGS-based, tumor-informed ctDNA detection. The approach delivers specific detection even when the SV catalogos are established from FFPE samples. The SV framework can stand alone or enhance SNV-based analysis pipelines.

Humans↗

PubMedDate not supplied

Somatic inactivation of genes on chromosome 13 is a common event in retinoblastoma.

Through family studies and analysis of patients with congenital chromosome abnormalities, the germ-line mutation responsible for the hereditary form of the eye tumour, retinoblastoma, has been assigned to the q14 region on chromosome 13 and closely linked to an enzyme called esterase D (ESD). Knudson has proposed that as few as one somatic event in addition to the germ-line mutation is required to induce tumours in patients with the hereditary form of retinoblastoma; the non-hereditary form requires two somatic events to occur in the same cell. The somatic event(s) may involve either mutation of the remaining normal gene at 13q14 or mutation of a gene at another site in the genome. Here we have examined six retinoblastoma patients who are heterozygous for electrophoretic variants of ESD. Although the normal cells of all six patients expressed both variants, the tumour cells of four patients expressed enzyme from only one of the two ESD alleles. We tentatively conclude that induction of a retinoblastoma tumour requires the somatic inactivation of genes near the ESD locus including the remaining normal gene at the retinoblastoma (RB) locus.

Cell Line↗

PubMed1995

Frequent loss of heterozygosity on chromosome 9, and low incidence of mutations of cyclin-dependent kinase inhibitors p15 (MTS2) and p16 (MTS1) genes in gliomas.

Four cyclin-dependent kinase inhibitors called p15, p16, p21 and p27 have been identified in mammals. Because these proteins participate in the control of cell cycle, they are potential targets for somatic mutations during carcinogenesis. In order to document the prevalence of p15 and p16 alterations in gliomas, we looked for loss of heterozygosity of chromosome 9p where these genes are localized. Allelic losses were observed in 31 of 44 investigated cases. In all cases they involved the p15/p16 locus. We then looked for mutations in the p16 and p15 genes in 46 gliomas. A total of three DNA variants were observed which were all present in the matched constitutional DNA. They may be unrelated to tumor development. A single somatic mutation was detected. It involved a C to G substitution in codon 93 of p16 and is predicted to change a threonine into an arginine. Taken together, these data indicate that inactivation by point mutation of these two cyclin-dependent kinase inhibitors is uncommon in glial tumor carcinogenesis, but that there may be a tumor suppressor gene on 9p in the vicinity of p16 and p15 genes.

Base Sequence↗

PubMed2026

nf-core/pacsomatic: a scalable somatic analytic pipeline using PacBio HiFi data.

MOTIVATION: Pacific Biosciences (PacBio) HiFi long-read sequencing enables robust characterization of complex genomic regions, repetitive elements, and structural variants (SVs) that are often inaccessible to short-read technologies. To fully leverage HiFi reads to advance cancer genomics and epigenetics, researchers require an end-to-end, scalable and optimized bioinformatics workflow. The nf-core framework meets this need by providing rigorously tested, community-curated pipelines that ensure reproducibility, transparency, and broad compatibility across computational environments. RESULTS: We present nf-core/pacsomatic, an automated Nextflow DSL2 pipeline designed for comprehensive paired tumor-normal somatic analysis using PacBio HiFi data. The workflow includes steps for read alignments against reference genome, somatic SNV/indel, SV, and CNV calling, CpG methylation profiling and differential methylation region (DMR) detection. Additional downstream modules support functional annotation, mutational signature analysis, tumor purity and ploidy estimation, and homologous recombination deficiency (HRD) assessment. Utilizing nf-core's modular design and containerized execution, nf-core/pacsomatic provides a stable framework for the reproducible discovery of biological insights. AVAILABILITY: nf-core/pacsomatic is available under the MIT License at nf-core (https://nf-co.re/pacsomatic) and github (https://github.com/nf-core/pacsomatic).

Software↗

PubMed1990

Three genes under different developmental control encode elongation factor 1-alpha in Xenopus laevis.

We have cloned cDNAs encoding two variants of the elongation factor for protein synthesis in Xenopus laevis, called EF-1 alpha. One of these (42Sp50) is expressed exclusively in immature oocytes. It is one of two protein components of a 42S RNP particle that is very abundant in previtellogenic oocytes. The 42S RNP particle consists of various tRNAs, 5S RNA, 42Sp50 and a 5S RNA binding protein (42Sp43). A major function served by 42Sp50 appears to be the storage of tRNAs for later use in oogenesis and early embryogenesis. The second EF-1 alpha variant (EF-1 alpha O) is expressed mainly in oocytes but transiently in early embryogenesis as well. Its mRNA cannot be detected after neurulation in somatic cells. EF-1 alpha O is closely related to a third EF-1 alpha (EF-1 alpha S), discovered originally by Krieg et al. (1). EF-1 alpha S is expressed at low levels in oocytes but actively in somatic cells. The latter two proteins are very similar to known eukaryotic EF-1 alpha from other organisms and presumably function in their respective cell types to support protein synthesis.

Amino Acid Sequence↗

PubMed2001

Idiopathic infertility in married couples in the light of cytogenetic analysis and sperm penetration assay.

We have selected 47 couples with unexplained infertility in order to analyse a possible link between sperm dysfunction studied in males in in vitro conditions and karyotype analysis of somatic cells. In order to identify so called "idiopathically infertile" couples we had to exclude any change in reproductive organs in both partners or in spermiogram which would qualify any of spouses into known category of infertility. We have revealed chromosome aberrations (translocations and marker chromosomes) in 19% of infertile males and in 6% of infertile females. Idiopathically infertile males had an overall decreased ability of sperm function (measured by proportion of penetrated hamster oocytes by human sperm) in comparison to fertile controls, however, still well placed within physiological range of values. Only sperm from a patient with identified translocation was clearly below the normal level of penetration (20% of penetrated oocytes), however, also the patients with revealed chromosome variant polymorphisms presented statistically lower values of penetration in comparison to fertile controls (39% vs 57%, p<0.05). On the contrary, patients with marker chromosomes did not exhibit affected sperm function. It can be speculated that only particular chromosome aberration in group of idiopathically infertile males may affect sperm functional capability (measured in vitro), however, the intragonadal genetic analysis has to be recommended in order to confirm such a causative link.

Adult↗

PubMed2006

A spindle cell variant of diffuse large B-cell lymphoma possesses genotypic and phenotypic markers characteristic of a germinal center B-cell origin.

Lymphoma with prominent spindle cell features, the so-called spindle cell lymphoma, is an unusual morphological variant of diffuse large B-cell lymphoma. Five new cases of spindle cell lymphoma have been analyzed by a multiparameter approach in order to clarify its clinical and biological features. All patients presented advanced stage disease with extranodal involvement. Vagina was the most common extranodal site. All patients received chemotherapy and are alive in complete remission. Morphologically, all five cases exhibited proliferation of spindle cells with a vaguely storiform pattern highly suggestive of spindle cell neoplasms of nonlymphoid origin. In contrast, the results of immunohistochemical analysis indicated that all five cases were hematolymphoid neoplasms of the B-cell lineage. These lymphomas consisted of a B-cell clonal population which exhibited somatic immunoglobulin and BCL-6 mutations as well as BCL-6 protein expression. The neoplastic spindle cells therefore closely resemble B cells residing in the germinal center. The absence of MUM1 expression in neoplastic spindle cells suggested that neoplastic spindle cells may be related to the early phases of intragerminal center maturation of B cells. The germinal center phenotype, with restricted expression of BCL-6, was associated with the presence of a primary extranodal origin, normal lactate dehydrogenase levels, and good response to treatment.

Adult↗

PubMed2026

Genome-wide detection of human 5' UTR variants that impact protein translation.

The 5' untranslated region (5' UTR) of messenger RNAs (mRNAs) plays a central role in regulating protein synthesis initiation, particularly through the Kozak sequence and upstream open reading frames (uORFs). Genetic variants within these regulatory elements could affect translation, altering gene expression and contributing to clinical phenotypes in humans. We developed a computational method called 5ULTRA (5' Untranslated Region Annotation) for analysis of whole-exome sequencing and whole-genome sequencing data to detect, annotate, and prioritize 5' UTR variants with potential translation impact. 5ULTRA identifies single-nucleotide variants, indels, and splicing variants that affect uORFs by creating or disrupting start/stop codons and that alter Kozak sequence strength of either the uORFs or the main coding sequence. 5ULTRA incorporates recent uORF databases and provides comprehensive annotations. 5ULTRA implements a machine-learning score to prioritize candidate variants with predicted effects on translation and also provides specific mechanistic predictions. The score correlates strongly with experimentally measured protein-level effects of 5' UTR variants. We applied 5ULTRA to multiple genetics datasets across diverse disease contexts, identifying candidate variants including potential cancer-driving somatic mutations predicted to decrease ABI1 level or increase NRAS abundance; common variants associated with traits such as multiple sclerosis, lung function, and cardiovascular function, by altering protein levels of TAGAP, VRTN, and SPAAR, respectively; and rare germline variants in our cohort, including a splicing variant of RPSA leading to 5' UTR sequence alteration that causes congenital asplenia and a variant of TNF that could predispose to tuberculosis.

Humans↗

PubMed2006

Mutation detection in tumor suppressor genes using archival tissue specimens.

Tuberous sclerosis complex (TSC) is a neurocutaneous syndrome characterized by seizures, mental retardation, and benign tumors of many organs, including the brain, kidneys, skin, retina, and heart. TSC is caused by mutations in the TSC1 and TSC2 tumor suppressor genes. The genes follow the two-hit model for tumorigenesis, with germline mutations inactivating one allele and somatic mutations inactivating the remaining wild-type allele. Allelic loss (also called loss of heterozygosity [LOH]) in the 9q34 and 16p13 regions has been found in many tumor types from TSC patients. Cardiac rhabdomyomas are frequently found in infants with TSC. Because rhabdomyomas often spontaneously regress, access to fresh tissue is limited. In this chapter, we present methodology for detection of genetic inactivation of TSC1 and TSC2 in paraffin-embedded archival tissues. The template DNA is obtained either by direct scraping of tissue or after laser capture microdissection. LOH analysis is performed after polymerase chain reaction amplification of microsatellite markers in the 9q34 and 16p13 regions and denaturing polyacrylamide gel electrophoresis. Mutation detection is performed using single-strand conformation polymorphisms on mutation detection enhancement gels. Finally, variant bands are amplified and analyzed by direct sequencing.

DNA↗