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PubMed2025

Genomic testing for RET in the clinic: UK and global perspective.

RET is a key oncogene in neuroendocrine cancer. Pathogenic germline variants lead to multiple different phenotypes, including multiple endocrine neoplasia type 2, medullary thyroid cancer (MTC), Hirschsprung disease and kidney malformations. Pathogenic somatic variants are also associated with MTC, and RET rearrangements are observed in papillary thyroid cancer, non-small cell lung cancer and pan-cancer syndromes. Testing for both germline and somatic variants is now feasible in everyday clinical practice, and their identification has important clinical consequences, both for affected individuals and their families. This mini-review will discuss current germline and somatic testing strategies in the UK and worldwide, as well as reporting and test outcomes (including variants of uncertain significance or incidental findings). It will explore actions following identification of a pathogenic germline variant, including predictive, reproductive and childhood testing, and somatic testing of RET variants in solid tumours informing personalised cancer treatment. Finally, it will discuss the challenge of delivering rapid and equitable access to genomic testing to ensure that all individuals can benefit promptly and appropriately to improve clinical outcomes.

Humans↗
PubMed1987

Growth and metastasis in allogeneic hosts. Lack of H-2-negative or somatic hybrid variant selection.

In vitro cultured B16 melanoma cells, which were previously found to have an impaired expression of H-2Kb and Db (as evaluated by antisera absorption assay), were used to study growth and metastasis in allogeneic mice in relation to H-2 expression. The possible emergence of somatic hybrids with host cells was also examined. B16-A cells grown subcutaneously in allogeneic BALB/c mice (H-2d) did not show a lack of H-2b expression, nor the acquirement of H-2d antigens was found. Spontaneous lung metastases were found in about 30% of BALB/c mice with progressing B16 tumor. Single lung metastases showed higher H-2b levels than cells from the respective tumors, and did not express host H-2 antigens. Tumor take was concomitant to the rise of an anti-H-2b humoral response: disease outcome was independent from the serum titer. B16-A cells injected intravenously in BALB/c mice gave rise to lung colonies; different colonies showed a wide range of H-2b antigens levels and no H-2d expression. Lung colonization capacity in normal allogeneic BALB/c mice was significantly higher than in syngeneic C57BL/6 mice. Both syngeneic and allogeneic mice, when pretreated with cyclophosphamide (CY) to reduce natural killer cell activity, showed a significant increase in lung colonization by B16-A cells. CY-treated C57BL/6 mice showed significantly higher numbers of lung colonies than CY-treated BALB/c mice. In conclusion, B16 growth and metastasis in the allogeneic environment do not seem to be determined by a selection of H-2-negative variants or by the emergence of somatic hybrids with host cells.

Animals↗
PubMed2024

ASXL1 truncating variants in BOS and myeloid leukemia drive shared disruption of Wnt-signaling pathways but have differential isoform usage of RUNX3.

BACKGROUND: Rare variants in epigenes (a.k.a. chromatin modifiers), a class of genes that control epigenetic regulation, are commonly identified in both pediatric neurodevelopmental syndromes and as somatic variants in cancer. However, little is known about the extent of the shared disruption of signaling pathways by the same epigene across different diseases. To address this, we study an epigene, Additional Sex Combs-like 1 (ASXL1), where truncating heterozygous variants cause Bohring-Opitz syndrome (BOS, OMIM #605039), a germline neurodevelopmental disorder, while somatic variants are driver events in acute myeloid leukemia (AML). No BOS patients have been reported to have AML. METHODS: This study explores common pathways dysregulated by ASXL1 variants in patients with BOS and AML. We analyzed whole blood transcriptomic and DNA methylation data from patients with BOS and AML with ASXL1-variant (AML-ASXL1) and examined differential exon usage and cell proportions. RESULTS: Our analyses identified common molecular signatures between BOS and AML-ASXL1 and highlighted key biomarkers, including VANGL2, GRIK5 and GREM2, that are dysregulated across samples with ASXL1 variants, regardless of disease type. Notably, our data revealed significant de-repression of posterior homeobox A (HOXA) genes and upregulation of Wnt-signaling and hematopoietic regulator HOXB4. While we discovered many shared epigenetic and transcriptomic features, we also identified differential splice isoforms in RUNX3 where the long isoform, p46, is preferentially expressed in BOS, while the shorter p44 isoform is expressed in AML-ASXL1. CONCLUSION: Our findings highlight the strong effects of ASXL1 variants that supersede cell-type and even disease states. This is the first direct comparison of transcriptomic and methylation profiles driven by pathogenic variants in a chromatin modifier gene in distinct diseases. Similar to RASopathies, in which pathogenic variants in many genes lead to overlapping phenotypes that can be treated by inhibiting a common pathway, our data identifies common pathways for ASXL1 variants that can be targeted for both disease states. Comparative approaches of high-penetrance genetic variants across cell types and disease states can identify targetable pathways to treat multiple diseases. Finally, our work highlights the connections of epigenes, such as ASXL1, to an underlying stem-cell state in both early development and in malignancy.

Humans↗
PubMed2006

Increased glycophorin A somatic cell variant frequency in arsenic-exposed patients of Guizhou, China.

Exposure to arsenic through domestic burning arsenic-containing coal causes various tumors in a population of Guizhou, China. The glycophorin A (GPA) assay is a human mutation assay detecting somatic variation in erythrocytes expressing the MN blood type, and was used to assess genotoxicity of arsenic-exposed patients. Peripheral blood was collected from 18 adult healthy subjects and 40 arsenic-exposed patients in heparin-treated tubes. Erythrocytes were isolated, fixed in formalin and immuno-labeled with fluorescent antibodies against GPA, followed by flow cytometry analysis. Arsenic exposure increased the variant frequency (expressed as the number of variant red cells per 10(6) erythrocytes): NN, 3.7 in healthy subjects versus 21.2 in arsenic-exposed patients; N phi, 12.6 versus 33.1; MM, 13.1 versus 110; and M phi, 5.2 versus 20.3. The total GPA variant frequency was increased about five-fold (34.7 in healthy subjects versus 185 in arsenosis patients). Furthermore, the variant frequency was significantly higher in skin tumor-bearing patients: NN, 19.4 in arsenic-exposed non-tumor patients versus 31.5 in tumor-bearing patients; N phi, 29.5 versus 54.5; MM, 102 versus 159; M phi, 15.9 versus 45.1. Total GPA variant frequency in arsenic-exposed patients bearing skin tumors was significantly increased compared to patients without skin tumors (167 versus 290). The relationship between arsenic exposure history and GPA variant frequency was less evident. These data demonstrate that arsenic exposure is associated with mutations at the GPA locus, an effect exaggerated in patients bearing arsenic-induced skin tumors. The variant frequency of GPA could be a useful biomarker for arsenic exposure and arsenic carcinogenesis.

Adult↗
PubMed1993

An analysis of idiotype expression in a high-affinity, somatically mutated variant of a germline-encoded anti-p-azobenzenearsonate antibody.

Using two polyclonal (rabbit) and two monoclonal anti-idiotype (anti-Id) reagents, we investigated structural correlates of the Id of mAb 36-71, a somatically mutated member of the CRIA Id family that has an exceptionally high affinity for the p-azobenzenearsonate (Ars) hapten. The two monoclonal anti-Ids reacted principally with the L chain of 36-71. The polyclonal anti-Ids interacted with both the H and L chain. The amino acid sequences of the VH and VL regions of 36-71 differ in eight and 11 positions respectively from those of the anti-Ars mAb 36-65, an unmutated prototype of the CRIA family. In the presence of 36-71L only three substitutions in 36-65 VH, introduced by mutagenesis, sufficed to restore full expression of the 36-71 Id. The same three substitutions had previously been shown to increase the affinity of 36-65 by a factor of 200, to a level equivalent to that of 36-71. X-ray crystallography had indicated that two of these substitutions introduce conformational changes consistent with the increase in affinity. We propose that these conformational changes may also account for the critical role of the three amino acids in Id expression. We also found that 36-65 is a very poor inhibitor of the interaction of 36-71 with its polyclonal anti-Ids, despite identity of the hapten-contacting residues in the two mAbs and evidence (from hapten inhibition) that the hapten-binding region is part of an important Id. Again, a difference in conformation at the binding site of the two mAbs could account for these observations.

Amino Acid Sequence↗
PubMed1980

Chromatin repeat length correlates with phenotypic expression in hepatoma cells, their dedifferentiated variants, and somatic hybrids.

Chromatin repeat length is known to differ among the tissues of organisms. We have examined the repeat length of somatic cells in culture and have found an unexpected correlation between this parameter and the state of differentiation of the cells. Three sequentially derived subclones of a rat hepatoma, similar in phenotype, present a constant repeat length of 189 (+/- 1) base pairs. Three independent variant clones do not express hepatic functions and each has a different repeat length: 184 base pairs, 188 base pairs, and 192 base pairs. Somatic hybrids between the two types of cells in which liver functions are extinguished have a repeat length close or identical to that of the nonexpressing parent. In the case of one hybrid clone that reexpresses the liver phenotype and has undergone some chromosome loss, the 189-base-pair repeat length characteristic of the well-differentiated cells is reestablished. Finally, an amelanotic variant clone derived from a pigmented hamster melanoma clone also shows a signficantly altered repeat length. No correlations have been observed between repeat length and either generation time or chromosome number. Maintenance of the expression of differentiation therefore appears to be associated with a constant repeat length, and loss of the former with a modification in repeat length, suggesting that chromatin packaging is intimately involved in the regulation of gene expression.

Animals↗
PubMed2025

Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair.

The Genome in a Bottle Consortium (GIAB), hosted by the National Institute of Standards and Technology (NIST), is developing new matched tumor-normal samples, the first explicitly consented for public dissemination of genomic data and cell lines. Here, we describe a comprehensive genomic dataset from the first individual, HG008, including DNA from an adherent, epithelial-like pancreatic ductal adenocarcinoma (PDAC) tumor cell line and matched normal cells from duodenal and pancreatic tissues. Data for the tumor-normal matched samples comes from seventeen distinct state-of-the-art whole genome measurement technologies, including high depth short and long-read bulk whole genome sequencing (WGS), single cell WGS, Hi-C, and karyotyping. These data will be used by the GIAB Consortium to develop matched tumor-normal benchmarks for somatic variant detection. We expect these data to facilitate innovation for whole genome measurement technologies, de novo assembly of tumor and normal genomes, and bioinformatic tools to identify small and structural somatic variants. This first-of-its-kind broadly consented open-access resource will facilitate further understanding of sequencing methods used for cancer biology.

Humans↗
PubMed1999

Rheumatoid factor isotype switch and somatic mutation variants within rheumatoid arthritis synovium.

The presence of clonally-related B-lymphocyte aggregates within synovial lining tisue of rheumatoid arthritis (RA) patients suggests a germinal centre-like reaction, which may hold implications for disease pathogenesis and the causes of chronic inflammation. We studied 250 rheumatoid factor (RF) heavy-chain sequences cloned from the synovium of three patients with RA, to determine whether they undergo both somatic mutation and isotype switching consistent with this hypothesis. Size analysis of immunoglobulin heavy-chain cDNAs from synovial RF+ B cells revealed oligoclonal RF+ populations and identically-sized VH-D-JH transcripts of different immunoglobulin isotypes. Sequencing of individual inserts selected from cloned immunoglobulin heavy-chain cDNAs demonstrated a clonal relationship between immunoglobulin M (IgM) RF and IgA RF, suggesting that this isotype switch occurred in synovium. Furthermore, most somatic mutations were found to have occurred after this isotype switch. This finding suggests that the RA synovial microenvironment sustains somatic mutation and isotype switching in RF-specific B lymphocytes akin to secondary lymphoid organs.

Aged↗
PubMed1987

Mitotic recombination between homologous chromosomes generates H-2 somatic cell variants in vitro.

A spontaneously arising variant clone that does not express the H-2Dd and H-2Ld molecules was isolated by immunoselection from an (H-2b X H-2d)F1 cell line. This variant clone expresses H-2Kb, H-2Db, and H-2Kd molecules. Southern blot analysis demonstrated that the variant was heterozygous at the H-2K, I, and S loci but had lost the H-2Dd and H-2Ld genes. Karyotype analysis showed that neither of the chromosome 17s in the variant had undergone detectable deletions. Quantitative Southern blot analysis demonstrated that the variant had two copies of the H-2Db gene, whereas the parental cell line had one copy of H-2Db. The loss of the H-2Ld and H-2Dd genes, accompanied by the attainment of homozygosity at H-2Db, is consistent with a recombination between the two chromosome 17 homologues. We conclude that although mitotic recombination between homologues has been difficult to demonstrate, it may not be infrequent and may account for the development of mutant genotypes in somatic cells in vitro. Such a mechanism occurring in vivo could result in the emergence of cells that are homozygous for deleterious alleles even though the individual may be constitutionally heterozygous.

Animals↗
PubMed1988

Regulation of idiotope expression. III. H-2 influences the magnitude and the idiotypy of a T-independent antibody response in mice of certain genetic backgrounds.

Antibody response to the phosphocholine (PC) epitope on Streptococcus pneumoniae R36a (Pn), a T-independent Ag type 2, was studied in H-2 congenic mouse strains. The PC-specific antibody plaque-forming cells (PFC) were enumerated in the spleen at various intervals after the primary Pn injection, and the proportion of PFC that produced antibody expressing the AB1-2 idiotope (Id) was determined by using the corresponding monoclonal anti-Id. AB1-2 is a cross-reactive Id, detectable on germline-encoded PC antibody of the T15 family, and on most, but not all, somatic variants of that antibody. The specific PFC responses in BALB/c (H-2d) and BALB.B (H-2b) strains were of comparable magnitude and most, if not all, PFC were ABl-1 Id-positive (AB1-2+). This was not the case in the responses of the B10D2 (H-2d) vs C57BL/10 (H-2b) strains and the D1.C (H-2d) vs D1.LP (H-2b) strains (on DBA/1 background). In each of these pairs, the H-2d mice were high responders, and the response was dominated by AB1-2 Id (greater than or equal to 80% AB1-2+ PFC at the peak, on day 5). The H-2b mice were low responders, and only a minor proportion of PFC (less than or equal to 30%) were AB1-2+; an increase of AB1-2+ was seen later in the response (d.10). The results of PFC assays were confirmed by measuring the PC-binding antibody and AB1-2 Id in the sera of D1.C and D1.LP mice immunized repeatedly with Pn. Moreover, D1.LP mice that had very low levels of AB1-2 Id had higher serum levels of antibody expressing two other T15 Id, B36-82, and B24-44. The B36-82 and B24-44 Id have been previously found on somatic variants of PC antibody expressed independently of the Ab1-2 Id. The concentrations of these two Id in D1.LP mice after repeated immunization approached those in D1.C. These results indicate that 1) the H-2 allelism may have a significant effect on TID antibody response in mice of a certain genetic background, but not in the BALB/c; and 2) the idiotypic repertoire of the response may be influenced by H-2 at the level of clonal variants of PC-reactive cells.

Alleles↗
PubMed2004

Effect of the codon 72 polymorphism (c.215G>C, p.Arg72Pro) in combination with somatic sequence variants in the TP53 gene on survival in patients with advanced ovarian carcinoma.

This study was conducted to evaluate the frequency and prognostic impact of TP53 alterations stratified for the TP53 codon 72 polymorphism (c.215G>C, p.Arg72Pro) in a cohort of 109 patients with advanced ovarian carcinomas. TP53 sequence variants were observed in 80 of the 109 (73.4%) tumors and were significantly associated with grade of differentiation (P=0.001). A tendency towards higher frequency of sequence variants in tumors with higher FIGO stages was seen (P=0.05). The type of TP53 sequence variant (transition A:T>G:C vs. G:C>A:T at CpG dinucleotides, and transversion G:C>T:A) had significant correlation with patients' age (P=0.04) with more A:T>G:C in patients over 60 years old. No significant associations were found between frequency of sequence variants and age at diagnosis, histological type, size of residual tumor after primary surgery, or long-term survival. Analyses of the codon 72 polymorphism in tumor DNA gave a higher frequency of homozygosity/hemizygosity than expected from the population frequency, particularly for the Pro allele. Tumors homozygous or hemizygous for the Pro allele had significantly higher frequency of TP53 sequence variants, particularly of the nonmissense type (P=0.002), and patients with these types of alterations had significantly shorter survival (P=0.04). TP53 protein accumulation, determined by immunohistochemistry (IHC), was found in 67.9% (74 out of 109) of the tumors, was significantly more common among serous than nonserous ovarian carcinomas (P=0.008), and had a significant effect on progression-free survival (P=0.03). p63 (TP73L; formerly TP63) and p73 (TP73) protein accumulation detected by IHC was seen in 67.9 and 0% of the tumors, respectively. A significantly higher frequency of p63-positive cases was seen among serous tumors (P=0.008) and tended to increase with increasing FIGO stages (P=0.05), but had no significant effect on survival. No association between p63 protein accumulation and TP53 protein accumulation was seen.

Adult↗
PubMed1986

Somatic cell variants of H-2Kb: a point mutation in the first extracellular domain results in altered immune recognition.

A cell-surface-associated variant H-2K product was expressed by an Abelson virus-induced pre-B-cell line after chemical mutagenesis with ethyl methane sulfonate. The variant cell line (R8.313) was previously demonstrated to have altered allodeterminants in Kb as demonstrated by both Kb-specific monoclonal antibody binding and alloreactive cytotoxic T lymphocyte (CTL) cytolysis. The mutant H-2Kb gene from R8.313 was cloned and characterized in detail. DNA sequence analysis of the region of the gene corresponding to the three extracellular domains identified a single point mutation resulting in a leucine-to-phenylalanine substitution at amino acid residue 82. The site of mutation within the alpha 1 domain was confirmed by oligonucleotide hybridization analysis. Mouse L-cell fibroblasts transfected with the mutant gene were recognized with the same monoclonal antibody binding and CTL lytic pattern as the R8.313 cell line, confirming that the altered phenotype of the mutant cell line was due to a point mutation in the H-2Kb gene. These data further extend the hypothesis that the region of amino acid residues 70-90 in the alpha 1 domain is important in the formation of both antibody and CTL-defined recognition structures on major histocompatibility complex class I molecules.

Animals↗
PubMed1991

Evaluation of somatic cell variants deficient in glycosylphosphatidyl-inositol anchoring as candidates for genetic correction.

Many cell surface glycoproteins are anchored in the lipid bilayer by a glycosylphosphatidyl-inositol (GPI) structure. Recently, a number of cell lines which are deficient in the biosynthesis and/or addition of this anchor have been described. In this report, we summarize the current knowledge on these lines and discuss their potential use to isolate the genes involved in the GPI anchor biosynthetic pathway with a specific emphasis on L cell fibroblasts.

Animals↗
PubMed1986

Somatic cell variants express altered H-2Kb allodeterminants recognized by cytolytic T cell clones.

The present studies have made use of in vitro derived H-2Kb mutants to analyze the fine specificity of alloreactive cytotoxic T lymphocytes (CTL). The variants were derived by negatively selecting mutagenized tumor cells with a monoclonal anti-H-2Kb antibody and positively selecting for residual cells expressing serologically altered H-2Kb molecules. Details of this procedure are described in the companion paper. Selected populations of bulk alloreactive and cloned CTL were examined for recognition of the variants. In contrast to the serologic findings presented in the companion paper, there does not appear to be a correlation between the monoclonal antibody used to select the R8 variant and the CTL specificities recognized. In several instances, CTL clones could discriminate between variants having identical serologic profiles. Therefore, it would appear that the CTL have a large repertoire of allorecognition, even when generated across a mutant anti-Kb combination reflecting only a few amino acid differences. In addition, a diverse set of epitopes can be recognized on the Kb molecule. Finally, in some instances a change in what would appear to be a single amino acid resulted in a profound alteration of CTL recognition even though the Kb mutant molecule expressed limited serologic changes. These results support the idea that small changes in the H-2Kb molecule can have dramatic effects on CTL even though there are relatively little effects on serologic recognition of the target molecule.

Animals↗
PubMed2026

Somatic likelihood tiering: an interpretable post-calling triage protocol for tumor-only whole-exome variant review.

Tumor-only whole-exome sequencing (WES) is used when matched normal tissue is unavailable, but one sample can produce thousands of variants. Somatic likelihood tiering (SLT) is an interpretable post-calling protocol that ranks Mutect2 calls into four review-priority tiers using population-frequency, germline-quality, cancer-knowledge, PureCN posterior, and clonal-hematopoiesis evidence. Layer 2 distinguishes common, rare-callable, and unevaluable gnomAD states; missing or unmatchable gnomAD evidence is not positive rarity evidence. On the SEQC2 HCC1395 benchmark, the callability-aware SLT-A row contained 101 calls, 78 truth variants, 77.2% PPV (95% Wilson confidence interval 68.1%-84.3%), and a Number Needed to Review (NNR) of 1.29 (1.19-1.47). The conservative SLT-C catchment retained 352 of 455 truth variants (77.4%, 73.3%-81.0%) and all tiers together retained 430 of 455 truth variants. SNV performance is the primary calibration frame: SLT-C retained 341 of 439 SNV truth variants, whereas indel results were exploratory because only 16 truth indels were available. Clinical cohorts are reported as recall and concordance versus partially dependent matched-normal Mutect2 references, not independent clinical sensitivity. Patient-level bootstrap intervals were principal: HdM-BLCA-1 SLT-A recall was 18.2% (14.0%-23.5%), and LUAD-TW SLT-A recall was 49.1% (26.6%-63.3%) among 32 evaluable patients. The HdM-BLCA-1 median SLT-A queue remained 1277 variants per patient, so SLT reduces first-pass candidate counts but does not measure review time or eliminate FFPE candidate-count burden. SLT provides an auditable tumor-only WES review queue, not a substitute for matched-normal sequencing, independent orthogonal validation, or definitive somatic classification.

Humans↗