PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “variant calling”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 199 records · Page 11Linked to original sources
PubMed1993

BCL2 complex rearrangement in follicular lymphoma: translocation mbr/JH and deletion in the vcr region of the same BCL2 allele.

Two rearrangements affecting the same allele of the BCL2 gene were characterized by molecular analysis of an untreated follicular lymphoma. The first rearrangement interested the major breakpoint region (mbr) on chromosome 18 and a JH segment on chromosome 14. The other one was located at the 5' end of the BCL2 gene, in the so called variant cluster region (vcr), and consisted of a series of deletions that removed part of a DNA region where initiation of transcription normally occurs. Interestingly, both rearrangements involved the same BCL2 allele. The simultaneous presence of mbr (or mcr) translocations and of minor rearrangements in vcr has been previously suggested by restriction map analysis in a significant number of follicular lymphomas. The significance of these abnormalities on the oncogenic process is discussed.

Alleles↗
PubMedDate not supplied

Expression of CD44 in duct cell carcinomas and in intraductal neoplasms of the pancreas.

The expression of alternatively spliced CD44 isoforms, especially so-called variant exons v5 and v6, has been shown to correlate with the progression of a number of human cancers examined the expression of standard CD44 and CD44 variants with exons v5 and v6 in 28 cases of human pancreatic tumors (16 cases of invasive duct cell adenocarcinoma and 12 cases of intraductal neoplasms) by immunohistochemistry using exon specific monoclonal antibodies. The expression of standard CD44 was frequently observed in both invasive duct cell carcinomas and intraductal neoplasms. The expression of CD44 variants (v5 and v6) was also seen in almost all duct cell carcinomas. In contrast, intraductal neoplasms infrequently expressed CD44-v5 and -v6, particularly v6 exon. Expression of CD44-v5 and v6 was a common characteristic of invasive cancer, while it was not so prominent in intraductal neoplasm. These findings may be related to the invasiveness of duct cell carcinoma and/or the benign biological behavior of intraductal neoplasm of the pancreas.

Carcinoma, Ductal, Breast↗
PubMed1998

[Spongiform encephalopathies].

Mad cow crisis (Bovine Spongiform Encephalopathy) had many consequences on the regulatory framework in several fields. It is now obvious that the agent of bovine spongiform encephalopathy is transmissible to man, provoking a new condition which differs from the sporadic from of Creutzfedt-Jakob Disease (CJD) called variant or new variant (vCJD). This paper tries to review the most important new findings in the scientific field of spongiform encephalopathies.

Animals↗
PubMed2025

LYCEUM: learning to call copy number variants on low-coverage ancient genomes.

MOTIVATION: Copy number variants (CNVs) are pivotal in driving phenotypic variation that facilitates species adaptation. They are significant contributors to various disorders, making ancient genomes crucial for uncovering the genetic origins of disease susceptibility across populations. However, detecting CNVs in ancient DNA (aDNA) samples poses substantial challenges due to several factors: (i) aDNA is often highly degraded; (ii) contamination from microbial DNA and DNA from closely related species introduces additional noise into sequencing data; and finally, (iii) the typically low-coverage of aDNA renders accurate CNV detection particularly difficult. Conventional CNV calling algorithms, which are optimized for high-coverage read-depth signals, underperform under such conditions. RESULTS: To address these limitations, we introduce LYCEUM, the first machine learning-based CNV caller for aDNA. To overcome challenges related to data quality and scarcity, we employ a two-step training strategy. First, the model is pre-trained on whole genome sequencing data from the 1000 Genomes Project, teaching it CNV-calling capabilities similar to conventional methods. Next, the model is fine-tuned using high-confidence CNV calls derived from only a few existing high-coverage aDNA samples. During this stage, the model adapts to making CNV calls based on the downsampled read depth signals of the same aDNA samples. LYCEUM achieves accurate detection of CNVs even in typically low-coverage ancient genomes. We also observe that the segmental deletion calls made by LYCEUM show correlation with the demographic history of the samples and exhibit patterns of negative selection inline with natural selection. AVAILABILITY AND IMPLEMENTATION: LYCEUM is available at https://github.com/ciceklab/LYCEUM.

DNA Copy Number Variations↗
PubMed1994

Leiomyosarcoma with prominent osteoclast-like giant cells. Analysis of eight cases closely mimicking the so-called giant cell variant of malignant fibrous histiocytoma.

Eight cases of leiomyosarcoma with osteoclast-like giant cells, arising in deep soft tissue, and that mimicked closely the "giant cell variant of malignant fibrous histiocytoma (MFH)," have been studied morphologically and immunohistochemically. The age of the patients ranged from 7 to 88 years (mean, 66.2 years; median, 74 years); five were female patients. Three lesions arose in the lower limbs, two in the buttock, and one each in the shoulder, chest wall, and the floor of the mouth. Follow-up in one case revealed a local recurrence and in two cases systemic metastases. All cases showed, at least focally, interwoven spindle cell fascicles, with the cytologic features of smooth muscle cells, as well as strong positivity for alpha-smooth-muscle actin, muscle actin, and desmin. The morphologically benign osteoclast-like giant cells expressed CD68 but failed to stain with myogenic markers. The association of leiomyosarcoma with prominent osteoclast-like giant cells is not as uncommon as generally believed, being evident in 8.7% of the deep-seated nonvisceral leiomyosarcomas that we have studied. These results provide good evidence for myogenic differentiation in at least a subset of those tumors with morphologic features currently classified as the giant cell variant of MFH. Considering that at least some other reported cases of giant cell MFH appear to be a variant of extraskeletal osteosarcoma, we would suggest that lesions with this distinctive pattern should be more carefully classified according to their apparent line of differentiation.

Aged↗
PubMed1984

[Interphase chromatin in lymphocytes in sex differentiation disorders].

Interphase chromatin of peripheral lymphocytes was studied in patients aged 6 to 20 years with Turner and Morris's syndromes by AO labeled fluorometry using the authors' modification of DNP cell thermal denaturation. It was shown that the lymphocyte chromatin melting profiles represent the curves with seven maxima at the following temperatures: 47 degrees, 55 degrees, 65 (+/- 2)degrees, 78 (+/- 1)degrees, 82, 88 (+/- 1)degrees, 92 (+/- 2)degrees C (P less than 0.01). There were no statistically significant differences between clinically and karyotypically different groups either in the parallelism of the melting profiles or in the fluorescence intensity of AO connected with cell DNP. In the male control group, the similar curve was obtained for lymphocyte chromatin in 25 and for normal human spermatozoa in 100% of cases, i.e. deviation specificity was revealed in the lymphocyte melting profiles, from a "classical" normal variant to the so-called male variant with sex differentiation breaks (Turner, Morris and Klinefelter's syndromes). Possible cytogenetic mechanisms of breaks are discussed.

Adolescent↗
PubMed1981

Granuloblastomas of the stomach (so-called eosinophilic granulomas)-- a variant of fibrous histiocytomas?

25 cases of focal connective tissue proliferations in the submucosa of the stomach are presented. These lesions are termed "granuloblastomas" and have many features in common with so-called eosinophilic granulomas of the stomach. We found that granuloblastomas may be subdivided into two groups: (1) 8 cases are considered to be the result of the proliferation of a peculiar granulation tissue with abundant eosionophilic granulocytes, and (2) 17 cases show a more or less marked storiform pattern and the cellularity is constituted by fibroblasts and histiocytes as well as differing amounts of eosinophilic granulocytes. After discussing the concept of "fibrous histiocytomas" it is concluded that at least the second group of granuloblastomas may be interpreted as a pseudotumorous variant of fibrous histiocytomas. It remains to be clarified in future if submucosal neurofibromas can show the histological features of lesions which we designate granuloblastomas.

Adult↗
PubMed2002

Haplotype study of West European and North African Unverricht-Lundborg chromosomes: evidence for a few founder mutations.

Unverricht-Lundborg disease (ULD) is a progressive myoclonus epilepsy common in Finland and North Africa, and less common in Western Europe. ULD is mostly caused by expansion of a dodecamer repeat in the cystatin B gene ( CSTB) promoter. We performed a haplotype study of ULD chromosomes (ULDc) with the repeat expansion. We included 48 West European Caucasian (WEC) and 47 North African (NA) ULDc. We analysed eight markers flanking CSTB(GT10-D21S1890-D21S1885-D21S2040-D21S1259- CSTB-D21S1912-PFKL-D21S171) and one intragenic variant in the CSTB 3' UTR (A2575G). We observed a founder effect in most of the NA ULD patients, as 61.7% of the NA ULDc (29/47) shared the same haplotype, A1 (1-1-A-1-6-7), for markers D21S1885-D21S2040-A2575G-D21S1259-D21S1912-PFKL. Moreover, if we considered only the markers D21S1885, D21S2040, A2575G and D21S1259, 43 of the 47 NA ULDc shared the same alleles 1-1-A-1, haplotype A. As previously shown, the WEC ULDc were heterogeneous. However, the Baltic haplotype, A3 (5-1-1-A-1-1), was observed in ten WEC ULDc (20.8%) and the CSTB 3'UTR variant, which we called the Alps variant, was observed in 17 ULDc (35.4%). Finally, as almost all NA patients, like Scandinavian patients, were of the haplotype A, we assumed that there was an ancient common founder effect in NA and Baltic ULD patients. We estimated that the putative most recent common ancestral ULD carrier with this haplotype A must have existed about 2,500 years ago (100-150 generations). Finally, this work provides evidence for the existence of only a small number of founder mutations in ULD.

3' Untranslated Regions↗
PubMed1995

Primary structure of ovine alpha s1-caseins: localization of phosphorylation sites and characterization of genetic variants A, C and D.

The primary structures of ovine alpha s1-casein variants A, C and D (formerly called Welsh variant) were determined. Separation of variants from whole casein was achieved using a fast and reliable reversed-phase HPLC method. Extended structural characterization of the purified proteins using electrospray mass spectrometry, automated Edman degradation and peptide mapping by means of HPLC-fast atom bombardment-mass spectrometry demonstrated that the mature protein was a mixture of two molecular species that differed in the deletion of residues 141-148 and were therefore 199 and 191 residues long respectively. The 199 residue peptide chain, which accounted for approximately 80% of the entire translated alpha s1-casein, was as long as its caprine and bovine counterparts, and had a 98 and 89% degree of identity with those two proteins respectively. Nine serine residues (positions 12, 44, 46, 64 to 68 and 75) were fully phosphorylated in alpha s1-casein A, whereas Ser115 and Ser41 were phosphorylated by approximately 50 and approximately 20% respectively. The differences between the three genetic variants A, C and D were simple silent substitutions, which however involved the degree to which the protein was phosphorylated. Variant C differed from variant A in the substitution Ser13-->Pro13 which determined the loss of the phosphate group on site 12 of the protein chain, SerP12-->Ser12. A further substitution, SerP68-->Asn68 caused the disappearance of both phosphate groups in the phosphorylated residues Ser64 and Ser66 in variant D; in this last casein variant there was no evidence of phosphorylation at Ser41.

Amino Acid Sequence↗
PubMed2006

Variant maple syrup urine disease (MSUD)--the entire spectrum.

BACKGROUND: In the rare inborn autosomal recessive disorder maple syrup urine disease (MSUD) the accumulation of the branched-chain amino acids (BCAAs) and their metabolic products results in acute and chronic brain dysfunction. About 20% of the patients suffer from non-classic variant forms of MSUD of different clinical severity. AIM: Up to now variant cases have mostly been published as individual case reports; the aim of this study was to give a comparative description of 16 individuals (aged 6-30 years) with different forms of variant MSUD. METHODS: Laboratory data, information on clinical course and treatment as well as aspects of developmental, intellectual and social outcome were obtained retrospectively. Data from in vitro and in vivo methods measuring the degree of enzyme deficiency were included. RESULTS: In addition to a mild phenotype, which fits well into the so-called intermittent variant, and a more severe phenotype with a wider range from a mild variant to an almost classic form, which fits well into the so-called intermediate variant, we assume the existence of an asymptomatic, non-disease variant of MSUD. These clinical phenotypes are not unambiguously differentiable on the basis of biochemical parameters. CONCLUSION: A continuum of clinical severity from asymptomatic to very severe (border to classic) exists in variant MSUD. Apart from newborns with classic MSUD, also those with variant forms benefit from early diagnosis and start of adequate treatment.

Adolescent↗
PubMed2002

Tuning ligand affinity, specificity, and folding stability of an engineered lipocalin variant -- a so-called 'anticalin' -- using a molecular random approach.

Anticalins are prepared by reshaping the ligand pocket of a natural lipocalin via protein engineering in order to recognize a prescribed ligand. In this manner, the anticalin DigA with specificity for digoxigenin was previously derived from the bilin-binding protein (BBP), a natural lipocalin from Pieris brassicae. The four peptide loops that form its ligand-binding site were randomized and a cognate variant was selected from the resulting library. Here, we propose a concept for improving the ligand-binding properties of this anticalin in an in vitro affinity maturation process by step-wise randomization of restricted areas of the loop region. Following selection on digoxigenin-binding activity via phage display and colony screening, several DigA variants were thus obtained. The recombinant proteins were thoroughly characterized in terms of ligand affinity and specificity, secondary structure and thermal stability against unfolding. The variant DigA16/19, which carries several new mutations, exhibits clearly improved affinity for digoxigenin, with K(D)=12.4 nM. Hence, it is suitable as a sensitive reagent in biochemical detection experiments, especially when produced as a functional fusion protein with alkaline phosphatase as reporter enzyme. In addition, DigA16/19 possesses enhanced ligand specificity and recognizes part of the linker that was used for fixing the steroid group to a carrier protein. Finally, the digoxigenin-binding anticalins appear to have high physico-chemical stability, with T(m) values in the 70 degrees C range. Our present findings support the notion that anticalins provide a useful class of compact and robust ligand-receptor proteins that can be tailored for practical demands.

Alkaline Phosphatase↗
PubMed2001

Relevance of folate metabolism in the pathogenesis of colorectal cancer.

The purpose of this review is to outline the principal mechanisms involved in folate metabolism and how they may relate to the pathogenesis of colorectal cancer (CRC). In recent years, mild folate depletion (low normal level) has been associated with an increased risk of developing certain cancers, in particular colorectal neoplasia. The epidemiologic and mechanistic evidence linking folate deficiency with carcinogenesis is reviewed, with a particular emphasis on colorectal neoplasia. Methylenetetrahydrofolate reductase (MTHFR) is a critical folate metabolizing enzyme, and a functional polymorphic variant of this enzyme, the so-called thermolabile variant, caused by a C677T transition in the MTHFR gene, is common in the general population. This review critically examines the evidence that suggests that carriers of this C677T variant may be at increased risk of developing colorectal neoplasia. Although folate depletion may predispose to the initiation of the neoplastic process, folate supplementation, on the other hand, might potentiate the progression of an already established early neoplastic clone (eg, a colorectal adenoma). This could have potential public health implications, given an increasingly widespread policy of folate supplementation of food staples.

Adenoma↗
PubMed1997

Social context affects phee call production by nonreproductive common marmosets (Callithrix jacchus).

Common marmosets produce two variants of their long call (phee call) in different situations. Intergroup calls are produced in territorial situations, and intragroup separation calls are produced by marmosets isolated from group members. Marmoset groups frequently include postpubertal, nonreproductive members; their roles in the spontaneous production of territorial vocalizations is unclear. This study analyzed the production of home cage phee calls by nonreproductive, postpubertal marmosets while they were housed in their natal groups and after pairing with an opposite-sex conspecific. Additionally, the production of the separation phee call variant was assessed in both social conditions. The results indicated that the marmosets rarely produced home cage, or territorial, phee calls while they were natally housed. In contrast, both males and females produced the territorial phee call at a much higher rate as early as 4 days after pairing. Agematched females remaining in their natal groups throughout the study produced home cage phee calls infrequently. Most marmosets produced separation phee calls at a high rate after separation from either their natal group or a partner, suggesting that the makeup of a social group has little effect on an animal's motivation to reunite with conspecifics. These results suggest that the social environment has an important influence on the production of territorial phee calls.

Animals↗
PubMed1992

"Solid" variant of aneurysmal bone cyst.

A case of the so-called "solid" variant of aneurysmal bone cyst is reported. A 12-year-old girl with a few weeks' history of backache presented with a tender palpable mass located thoraco-spinal in the back at Th 3. Radiologically, the lesion was consistent with conventional aneurysmal bone cyst. Morphologically, it showed fibroblastic, fibrohistiocytic, fibromyxoid, osteoclastic and osteoblastic components as well as small aneurysmal sinusoids. Based on four other well documented cases, the clinico-pathological features and the differential diagnostical problems are discussed.

Bone Cysts↗
PubMed1980

Malignant lymphoma with a high content of epithelioid histiocytes: report of T-cell variant of so-called Lennert lymphoma and review of the literature.

The present report describes the first case of well-differentiated nodular lymphocytic lymphoma evolving into Lennert lymphoma of T-cell origin. A 58-year-old white female developed malignant lymphoma, well-differentiated, lymphocytic type, nodular, with focal bone marrow involvement (stage IV) in May 1975. She received 16 cycles of cyclophosphamide and prednisone combination chemotherapy which was completed in October 1976. A complete remission was achieved. In December 1976, she relapsed and was treated with cyclophosphamide, vincristine, bleomycin, and prednisone until May 1977. Lymphadenopathy decreased until August 1978, but then increased again. Biopsy of an axillary lymph node was interpreted as Lennert lymphoma. She received methotrexate, cyclophosphamide, vincristine, adriamycin, and prednisone beginning in September 1978. When last seen in November 1979, she was in partial remission. Lymphoid cells obtained from lymph node which was involved with Lennert lymphoma consisted of 93% standard E-rosettes and 83% gravity E-rosettes. Cytoplasmic immunoglobulin on frozen sections was negative, but acid phosphatase (ACP) and alpha-naphthyl acetate esterase reactions were strongly positive. These findings support a T-cell proliferation in Lennert lymphoma. A review of the literature reveals only four cases of Lennert lymphoma of T-cell origin.

Drug Therapy, Combination↗
PubMed2026

Long-read Sequences Mapped to a Complete Reference Genome Uncover Uncaptured Structural Variants across the Beta-globin Cluster in Africans with Sickle Cell Disease.

African genomes are marked by extensive complexity in the number and distribution of variants, yet remain under-represented in genetic databases and the human reference genome. This gap in representation limits the broad application of genomic medicine. Sickle cell disease (SCD) - one of the most common monogenic diseases - has its highest prevalence in Africa, and variation in disease severity has consistently been linked to the beta-globin locus, including levels of fetal hemoglobin (HbF). Modulation of HbF is central to current SCD gene therapies; however, the inherent complexity and variation at the locus in African genomes presents a challenge to translating these advances to Africa. Here, we align long-read single molecule sequences (LRS) targeted to the beta-globin region to the hg38 and T2T-CHM13v2 genome references in 40 individuals with SCD, predominantly recruited from three African countries. We demonstrate that the expanded T2T-CHM13v2 reference sequence at this locus reduces Structural Variant (SV) calls by 70% and uncovers uncaptured single nucleotide variants (SNVs). Across the cluster we report 343 SVs and 196 SNVs that have not been previously reported, including in LRS data from the All of Us project. By including African populations from ethnolinguistic groups that have not been previously surveyed we improve variant resolution and bolster evidence for observed variation. Finally, we identify a common ∼4kb insertion locus overlapping the HBB promoter among individuals with high HbF. These results demonstrate the utility of combining a comprehensive reference genome with LRS in African populations to uncover genomic variation at disease-associated loci.

SNV↗