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PubMed1987

Molecular cloning and differential expression of somatic and testis-specific H2B histone genes during rat spermatogenesis.

We have cloned cDNA of a testis-specific histone, TH2B (a variant of H2B), and rat somatic H2B gene to investigate regulation of testis-specific histone genes during rat spermatogenesis. The amino acid sequences deduced from DNA sequences show extensive sequence divergence in the N-terminal third of the two histones. The rest is highly conserved. One cysteine residue was found in TH2B. No cysteine is present in somatic histones except in H3 histone. We investigated the expression of TH2B and H2B genes using the regions of sequence divergence as hybridization probes. The TH2B gene is expressed only in the testis, and the expression of this gene is detected 14 days after birth, reaching a maximum at Day 20. The level of H2B mRNA shows a reciprocal pattern. This contrasting pattern can be explained by the gradually changing proportion of spermatogonia and spermatocytes with testicular maturation. In situ cytohybridization studies show that H2B gene is expressed primarily in proliferating spermatogonia and preleptotene spermatocytes, whereas TH2B gene is expressed exclusively in pachytene spermatocytes which first appear in testis about 14 days after birth. H2B and TH2B genes appear to be ideal markers for the study of proliferation and differentiation events in spermatogenesis and their regulatory mechanisms.

Amino Acid Sequence↗

PubMed2005

Pharmacogenetic analysis of human steroid 5 alpha reductase type II: comparison of finasteride and dutasteride.

Human steroid 5 alpha-reductase type II is a prostate-specific, membrane-associated enzyme that catalyzes the conversion of testosterone to dihydrotestosterone, the most potent androgen in the prostate gland. Genetic variants of this enzyme have been associated with both the development and the progression of prostate cancer. Both finasteride and dutasteride are competitive inhibitors of the type II steroid 5 alpha-reductase that have been effectively used for the treatment of benign prostatic hyperplasia. Finasteride has also been successfully utilized for prostate cancer chemoprevention. We here investigate 5 alpha-reductase inhibition assays in vitro to measure the effect of incubation time on the apparent inhibition constant (Ki) for both constitutional and somatic (prostate cancer) enzyme variants. Our systematic pharmacogenetic analysis shows that both finasteride and dutasteride are slow, time-dependent inhibitors of steroid 5 alpha-reductase type II, and that the inhibition kinetics depend on the 5 alpha-reductase genotype. We also show that, overall, dutasteride is a more efficient steroid 5 alpha-reductase inhibitor than finasteride. Based on our data, we are able to map areas of the enzyme that are responsible for this time-dependent inhibition for either (or both) enzyme inhibitor(s). This comprehensive pharmacogenetic analysis of steroid 5 alpha-reductase variants unveiled significant pharmacogenetic variation for both finasteride and dutasteride and thus should be taken into account when designing protocols for treatment and/or chemoprevention of prostatic diseases with either one of these 5 alpha-reductase inhibitors since there is considerable pharmacogenetic variation for both drugs.

3-Oxo-5-alpha-Steroid 4-Dehydrogenase↗

PubMed2003

Origin and development in vitro of shoot buds and somatic embryos from intact roots of Helianthus annuus x H. tuberosus.

A variant clone of the tetraploid (2n = 4x = 68) interspecific hybrid Helianthus annuus x H. tuberosus derived by in vitro tissue culture showed a deviation from the usual pattern of organization of the plant body. This variant developed shoot-like structures and somatic embryos from intact adventitious roots of in vitro-grown plantlets. The morphogenetic structures were not normally able to differentiate complete plants. They did show cellular proliferation with the inception of additional secondary embryos, leaf-like structures and unorganized masses of callus. Nevertheless, some ectopic structures isolated from roots and transferred onto fresh basal medium without growth regulators were able to produce plantlets that exhibited the same phenotype as the original clone. Histological analyses demonstrate that they originate from cortical cells in association with the development of lateral root primordia.

Culture Techniques↗

PubMed1998

Human in vivo somatic mutation measured at two loci: individuals with stably elevated background erythrocyte glycophorin A (gpa) variant frequencies exhibit normal T-lymphocyte hprt mutant frequencies.

A survey of glycophorin A (gpa) in vivo somatic cell mutation in a population of 394 healthy people from 8 to 77 years of age (mean age +/- SD 41 +/- 15 years) revealed a subset of 37 individuals with stably elevated allele-loss and/or allele-loss with duplication variant erythrocyte frequencies (Vf) exceeding 30 x 10(-6). These 37 individuals with gpa outlier Vf are significantly older (P < 0.001) than the remainder of the larger study population from which they were drawn reflecting a highly significant increase in the prevalence of these individuals in the population beyond age 40 years. A study of hpt mutant frequencies (Mf) in the peripheral blood T-lymphocytes of 27 of these individuals, together with 15 matched control individuals with unremarkable gpa Vf, was undertaken to determine if these subjects also displayed elevated mutation frequencies at this independent locus indicative of globally elevated somatic mutation. The hprt Mf in these 27 subjects (geometric mean 11.5 x 10(-6)(dispersion interval 5.8 x 10(-6) to 22.8 x 10(-6)) was not significantly different from that observed in the 15 controls (geometric mean 12.1 x 10(-6)(dispersion interval 5.7 x 10(-6) to 25.5 x 10(-6)). These Mf are higher than typically reported values reflecting the older age distribution of these individuals (arithmetic mean age +/- SD 53 +/- 12 and 50 +/- 16 years for the subjects and controls, respectively). Taken together, these data suggest that several genetic mechanisms may be responsible for producing the gpa outlier Vf observed in these subjects. The observation that hprt Mf were not increased indicates that the majority did not arise by a genome-wide increased rate of somatic mutation detectable at both loci. The fixation and subsequent expansion of 'jackpot' mutations at the gpa locus occurring early in embryonic/fetal development also does not appear to be a predominant mechanism. Some cases may result from a stable over-representation of gpa variant cells, perhaps associated with a marked age-dependent decrease in the number of contributing erythroid stem cells in the bone marrow. The subset that displays elevated allele-loss with duplication Vf involving both gpa alleles may represent individuals with increased rates of somatic recombination. Elevations arising by this mechanism are not detected in the hprt assay, but could be confirmed using a autosomal locus in vivo somatic cell mutation endpoint such as the hla-a assay. Of primary biological significance, these results demonstrate that genetics/stochastic processes leading to the loss of heterozygosity of somatic cells occur ubiquitously in humans and in some individuals this level of somatic mosaicism can approach a frequency of 10(-3) at the gpa locus in erythroid lineage cells.

Adolescent↗

PubMed1998

Efficacy and safety of fluvoxamine in body dysmorphic disorder.

BACKGROUND: Body dysmorphic disorder (BDD), a preoccupation with an imagined or slight defect in appearance, has been noted in case reports, retrospective studies, and clinical series to respond to serotonin reuptake inhibitors (SRIs). These data further suggest that the delusional variant of BDD (delusional disorder, somatic type) may also respond to SRIs. However, systematic pharmacologic treatment studies of BDD and its delusional variant are needed. METHOD: Thirty subjects with BDD or its delusional variant (DSM-IV) were prospectively treated in an open-label fashion with fluvoxamine for 16 weeks. Subjects were assessed at regular intervals with the Yale-Brown Obsessive Compulsive Scale Modified for BDD (BDD-YBOCS), the Clinical Global Impressions (CGI) scale, the Hamilton Rating Scale for Depression, the Brown Assessment of Beliefs Scale, and other measures. RESULTS: BDD-YBOCS scores (mean +/- SD) decreased from 31.1 +/- 5.4 at baseline to 16.9 +/- 11.8 at termination (p < .001). Nineteen (63.3%) subjects were rated as responders on the BDD-YBOCS and the CGI (10 [33.3%] were much improved, and 9 [30.0%] were very much improved). Delusional subjects were as likely to respond to fluvoxamine as nondelusional subjects, and delusionality significantly improved. All 5 responders who were delusional at baseline were no longer delusional at study endpoint. The mean dose of fluvoxamine was 238.3 +/- 85.8 mg/day, and mean time to response was 6.1 +/- 3.7 weeks. Fluvoxamine was generally well tolerated. CONCLUSION: These results suggest that fluvoxamine is a safe and effective treatment for BDD, including its delusional disorder variant. Controlled treatment trials are needed to confirm these findings.

Adult↗

PubMed1993

Body dysmorphic disorder: does it have a psychotic subtype?

BACKGROUND: Although body dysmorphic disorder (BDD) is classified in DSM-III-R as a nonpsychotic somatoform disorder, controversy exists as to whether BDD can present with psychotic features. If it can, this raises the possibility that its DSM-III-R psychotic counterpart-delusional disorder, somatic type--may not be a separate disorder. The purpose of this study was to determine whether patients with nonpsychotic BDD (defined according to DSM-III-R criteria, i.e., with maintenance of some insight) were different from patients with psychotic BDD (those whose preoccupation was without insight and of delusional intensity). METHOD: Fifty consecutive patients meeting DSM-III-R criteria A and C for BDD were assessed with a semistructured interview and the Structured Clinical Interview for DSM-III-R (SCID). Family histories of psychiatric disorders were blindly assessed. The 24 patients with nonpsychotic BDD were compared with the 26 patients with psychotic BDD with respect to demographics, phenomenology, course of illness, associated features, comorbid psychiatric disorders, family history, and treatment response. RESULTS: Patients with psychotic BDD displayed a significantly higher rate of lifetime DSM-III-R psychotic disorder diagnoses than patients with nonpsychotic BDD. However, the two groups did not differ significantly on most other variables examined. For instance, both psychotic and nonpsychotic patients displayed significant morbidity; high comorbidity with mood, anxiety, and psychoactive substance use disorders; and apparent preferential response to serotonin reuptake inhibitors rather than to non-serotonin reuptake blocking antidepressants or antipsychotics. CONCLUSION: Body dysmorphic disorder may have a closely related psychotic subtype that significantly overlaps with, or may even be the same disorder as, the BDD variant of delusional disorder, somatic type. Inclusion of a psychotic subtype for BDD should be considered for future editions of DSM.

Adult↗

PubMed1998

Somatic instability of the APC I1307K allele in colorectal neoplasia.

The adenomatous polyposis coli (APC) gene is proposed to function as a gatekeeper of colorectal neoplasia. A germ-line variant of this gene, the APC I1307K allele, is present in approximately 6% of the Ashkenazi Jewish population. To assess the role in tumorigenesis of the variant (A)8 tract produced by this allele, we undertook a somatic mutation analysis of the region surrounding codon 1307 in colorectal tumors from APC I1307K carriers. Somatic mutations involving the variant (A)8 tract were identified in 53 of 127 (42%) tumors from APC I1307K carriers compared with 5 of 127 (4%) mutations involving the wild-type allele of these tumors (P < 0.0001). Loss of heterozygosity of the wild-type allele was significantly more common in tumors with APC I1307K allele mutations (25 of 41, 61%) compared with APC I1307K carrier tumors without mutation of the variant (A)8 tract (12 of 53, 23%; P < 0.0005). This somatic biallelic APC inactivation further confirms the biological importance of the I1307K germ-line variant. The vast majority of APC I1307K somatic mutations consisted of a single adenine insertion (insA) involving the variant (A)8 tract. This insA mutation was mutually exclusive of the presence of microsatellite instability with 0 of 49 tumors with insA displaying BAT-26 instability compared with 9 of 78 tumors without insA (P=0.01). These findings support a model where somatic instability of the (A)8 tract produced by the APC I1307K allele leads to increased APC gene inactivation and directly accounts for 42% of the colorectal neoplasms occurring in APC I1307K carriers.

Adenomatous Polyposis Coli↗

PubMed2026

Recurrent patterns of TOP1-mediated neuronal genomic damage shared by major neurodegenerative disorders.

Amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and Alzheimer's disease (AD) represent two major categories of neurodegenerative disorders-TAR DNA-binding protein 43 (TDP-43) and tau proteinopathies-for which the mechanisms driving neuronal death remain unclear. Single-cell whole-genome sequencing of 469 neurons from C9ORF72 ALS, C9ORF72 FTD, AD, and control brains revealed increased somatic single-nucleotide variants (sSNVs) and insertions/deletions (sIndels) in all three diseases. Mutational signature analysis identified a disease-associated sSNV signature consistent with oxidative damage and an sIndel process affecting 22% of ALS, 76% of FTD, and 61% of AD neurons-but only 2% of control neurons-resembling signature ID4, previously linked to topoisomerase 1 (TOP1)-mediated mutagenesis. Rapid approach to DNA adduct recovery (RADAR) assays confirmed increased TOP1-DNA covalent complexes, and duplex sequencing confirmed the increased sIndels and identified single-strand events as likely precursor lesions. TOP1-associated sIndel mutagenesis and genome instability thus represent a mechanism shared by both TDP-43 and tau neurodegeneration.

Humans↗

PubMed2025

Combined somatic mutation and transcriptome analysis reveals region-specific differences in clonal architecture in human cortex.

The human cerebral cortex is specialized into regions, but little is known about how human cellular lineages shape cortical regional variation and neuronal cell-type distribution during development. Here, we map single-cell lineages of human cortical regions and neuronal subtypes using >1,000 somatic single-nucleotide variants (sSNVs) identified from deep bulk whole-genome sequencing and analyzed over 25 regions and >72,000 single cells. In the fronto-parietal cortex, sSNVs are rarely restricted, marking neuron-generating clones that disperse into neighboring regions. In contrast, the primary visual cortex harbors 30%-70% more sSNVs than the neighboring secondary visual cortex. Clones at this border exhibit more restricted dispersion, suggesting late developmental lineage segregation. Single-nucleus sSNV and whole-transcriptome analysis reveal glutamatergic neuron clones with modest regional restrictions that share low-mosaic sSNVs with some GABAergic neurons, suggesting a recent dorsal cortical progenitor. Our analysis reveals human-specific cortical lineage patterns, regional differences in clonal patterns, and late divergence of some glutamatergic/GABAergic lineages.

Humans↗

PubMed1985

Background allelic variants in normal hemopoietic cells and Bloom's syndrome erythrocytes and the possible implication of somatic crossingover.

The existence of rare cells with blood group A or B phenotype among the red cells of AB heterozygotes is a well-known phenomenon. However, its origin remains unclear due to methodological problems. A direct quantitation of non-B and non-A erythrocytes in A1B donors revealed minor populations of only-A and only-B cells, respectively, both in a frequency of 10(-3). Null cells comprise, at the most, a fraction of about 5 X 10(5). In order to discriminate between somatic crossingover (SCO) and gene inactivation as the underlying mechanism, three individuals were selected who were double heterozygotes for the blood group (AB) and the linked locus of adenylate kinase (AK-2-1). Separation of cells with A or B phenotypes did not result in cosegregation of the AK isoenzymes. Thus, the variant blood group phenotypes represent the normal frequency of allelic silence, not the product of SCO. This sets a background variant level for the estimation of somatic recombination in blood cells from normal donors. Determination of variant phenotypes in a Bloom's syndrome patient, heterozygous for AB, gave a frequency six times higher than the value of normals. It is suggested that this elevated figure might indicate the frequency of SCO, which is known to be higher in Bloom's syndrome.

ABO Blood-Group System↗

PubMed1998

Expression of an embryonic fibronectin splicing variant in human masseter muscle.

Fibronectin is an extracellular matrix protein that is a key constituent of all skeletal muscles. Its deposition increases in a number of pathological conditions, including some muscular dystrophies in which a progressive increase in lower-face height is often noted. It has been shown in other organ systems that increased deposition of fibronectin is associated with changes in the expression of differentially spliced isoforms of the molecule. This investigation documents the expression of mRNA coding for fibronectin and its splicing variants, EIIIA and EIIIB, in biopsies of masseter muscle from normal and long-face patients, using reverse transcriptase-polymerase chain reaction. Expression was compared with that occurring in anatomically and embryologically differing somatic skeletal muscle. Masseter expressed fibronectin mRNA containing the EIIIA but not the EIIIB splicing variant. Conversely, somatic skeletal muscle expressed neither the EIIIA nor EIIIB variants. There were no differences between expression of fibronectin containing the EIIIA splicing variants in masseter from normal and long faces. These results suggest that variations in fibronectin expression reflect the differing functional demands of muscles from different anatomical locations and indicate that jaw and somatic muscle belong to different allotypes.

Base Sequence↗

PubMed1978

[Characteristics of the polysaccharide-containing somatic antigens isolated from the K-1 strain of the plague microbe and its antibiotic-resistant variants].

Immunochemical analysis of 2 polysaccharide-containing structures of the lypopolysaccharide of the plague causative agent (main somatic antigen and lipopolysaccharide) isolated from K-1 strain and a number of its antibiotic resistant mutants was carried out. It was shown that development of resistance to streptomycin alone or its combination with monomycin did not cause detectable changes in the monosaccharide composition and serological properties of the cultures tested. More significant changes associated with development of complex resistance, i.e. K-1 (Strr leads to Penr leads to Tetr) were accompanied by a decrease in the content of hexozamine and serological activity of the main somatic antigen determining the O-specificity of the lipopolysaccharide. Defective changes in the monosaccharide composition and serological properties of both the main somatic antigen and the polysaccharide were observed in the yellow variant of the streptomycin resistant mutant K-1.

Anti-Bacterial Agents↗

PubMed2025

Detection and Characterization of RB1 Mosaicism in Patients With Retinoblastoma Receiving cfDNA Test.

IMPORTANCE: Plasma cell-free DNA (cfDNA) testing is increasingly used for disease diagnosis and monitoring in retinoblastoma, with RB1 allele fraction in cfDNA actively corresponding to disease status and treatment response. However, while RB1 mosaicism has been reported in retinoblastoma, its clinical implications and potential impact on cfDNA testing remain unclear. OBJECTIVES: To identify RB1 mosaicism using paired plasma and buffy coat (containing lymphocytes, monocytes, granulocytes, and platelets) DNA testing, and to characterize the implications of RB1 mosaicism on cfDNA testing outcomes. DESIGN, SETTING, AND PARTICIPANTS: In this cross-sectional study, participants with retinoblastoma underwent testing with MSK-ACCESS (Memorial Sloan Kettering-Analysis of Circulating cfDNA to Examine Somatic Status), a clinical assay that combines plasma cfDNA and buffy coat genomic DNA sequencing, enabling the detection and differentiation of somatic, heterozygous, and mosaic variants, between July 2020 and April 2024 at the Memorial Sloan Kettering Cancer Center. Mosaic findings from MSK-ACCESS were correlated with those from a subgroup of patients who concurrently underwent testing using the MSK-IMPACT germline assay. Data analysis was performed from April to September 2024. EXPOSURE: RB1 mosaicism in retinoblastoma. MAIN OUTCOMES AND MEASURES: The RB1 variant allele fractions in cfDNA and buffy coat genomic DNA were used to detect RB1 mosaicism. RESULTS: A total of 136 consecutive patients with retinoblastoma (median age at diagnosis, 1.0 year [IQR, 0.4-1.7 years]; 74 [54.4%] female; 67 with bilateral disease and 69 with unilateral disease) who underwent testing with the MSK-ACCESS assay were included. RB1 mosaicism was identified in buffy coat DNA from 20 patients (14.7%), with consistent results detected in all 11 participants tested concurrently by the MSK-IMPACT (Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets) germline assay. Four participants with RB1 mosaicism previously tested negative for germline RB1 variants by external laboratories. Compared with heterozygous participants, participants with RB1 mosaicism had a lower risk of developing bilateral disease (91.7% vs 55.0%, respectively; difference, 36.7% [95% CI, 13.8%-59.6%]; P = .002). In cfDNA, the mosaicism variant was detected both before and after treatment, with variant allele fraction initially decreasing after treatment but then stabilizing at levels consistent with mosaicism, despite the absence of clinical disease. CONCLUSIONS AND RELEVANCE: The accurate detection and quantification of RB1 mosaicism are crucial. RB1 mosaicism should be considered when RB1 variants persist in cfDNA after treatment without evidence of disease; failure to do so may lead to false-positive results and overtreatment in patients with RB1 mosaicism. Identifying RB1 mosaicism may improve patient counseling, inform treatment decisions, and enhance surveillance efforts.

Humans↗

PubMed2002

Dynamics of Dnmt1 methyltransferase expression and intracellular localization during oogenesis and preimplantation development.

The imprinting of mammalian genes depends on the maintenance of DNA methylation patterns during pre- and postimplantation development. Dnmt1o is a variant form of the somatically expressed Dnmt1 cytosine methyltransferase that is synthesized and stored in the oocyte cytoplasm and trafficks to the eight-cell nucleus during preimplantation development, where it maintains DNA methylation patterns on alleles of imprinted genes. Transcripts encoding Dnmt1 are present in preimplantation embryos, suggesting that Dnmt1 protein is also expressed in the preimplantation embryo, and may account for maintenance methylation at preimplantation stages other than the eight-cell embryo. However, using an antibody that detects Dnmt1, but not Dnmt1o, no Dnmt1 protein was detected on immunoblots or by immunocytochemical staining in wildtype preimplantation embryos. Moreover, Dnmt1 protein produced in the oocyte from a modified Dnmt1 allele, Dnmt1(1s/1o), trafficked to nuclei of eight-cell embryos, but not to nuclei of other stages. The highly restricted nuclear localization patterns of oocyte-derived Dnmt1o and Dnmt1 during preimplantation development add further support to the notion that DNA methyltransferases other than Dnmt1 are required for maintaining imprints during preimplantation development.

Alternative Splicing↗

PubMed1999

Genomic instability, DNA methylation, and natural selection in colorectal carcinogenesis.

Neoplastic transformation is increasingly understood in terms of evolutionary mechanisms, and it is now widely accepted that tumor progression involves natural selection of genetic variants occurring in the somatic environment. Here we give a review of data that substantiate this Darwinian view to tumorigenesis, with particular emphasis on recent advances related to colorectal cancer. We specifically focus on the controversies related to genomic instability and DNA methylation, and present a model, which interrelates these phenomena to the basic evolutionary concept of biology.

Cell Transformation, Neoplastic↗

PubMed1990

Nucleotide sequence of the gene for human transition protein 1 and its chromosomal localization on chromosome 2.

Transition protein 1 (TNP1) is a highly basic nuclear protein of 54 amino acids that is found in haploid spermatogenic cells during the period of transition of histones to protamines. Using the cDNA clone for human TNP1, we have isolated the gene encoding human TNP1 from human genomic libraries. The gene contains an intron of 200 bp; 1104 bp of the 5'- and 276 bp of the 3'-noncoding region have been sequenced. Comparison with the rat TNP1 gene yielded a similarity of 77% over the region between the transcription start point and the polyadenylation signal. The gene contains typical CAAT and TATAA boxes at conventional distances from the transcriptional start site. Using a series of human-rodent somatic cell hybrids containing variant complements of human chromosomes, the TNP1 gene was found to cosegregate with human chromosome 2. By in situ hybridization, the gene was assigned to the q35 and q36 bands of the long arm of chromosome 2. This chromosomal region encodes several genes, including TNP1, that are located on murine chromosome 1.

Amino Acid Sequence↗

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↗

PubMed2026

URMD-Seq: A high-throughput method for scalable detection of ultra-rare mutations in the human mitochondrial genome.

The study of mitochondrial genetics has long been limited to polymorphisms and high frequency mutations owing in part to technical and technological limitations in reliably detecting and quantifying rare somatic mutations. Over the past decade or so, the study of rare somatic mitochondrial DNA (mtDNA) variants has expanded and continues to garner increasing interest in a wide range of research fields. Here, we describe Ultra-Rare Mutation Detection-Sequencing (URMD-Seq), a high-throughput method that combines unique molecular identifier (UMI)-based library preparation and Next Generation Sequencing (NGS) for the accurate and scalable detection of ultra-rare mutations in the mtDNA control region. Our method exploits degenerate primers to label individual mtDNA molecules. This is followed by several purification, quantification and amplification steps, to obtain high quality amplicons for sequencing on the Illumina MiSeq platform. Our approach enables the use of total genomic DNA extract as starting point for the assay, overcoming the need for organelle isolation and/or mtDNA enrichment, hence broadening the type of specimen that can be studied, while offering cost and time benefits. The assay described herein has been demonstrated to reliably measure variants present at on average 0.09%, but as low as 0.03%, variant allele frequency in a variety of tissues, including fresh and frozen biobanked specimens. Using this protocol, library preparation of 300 specimens can be completed by a single individual with general nucleic acid handling experience in approximately 20 days. Given its flexibility and scalability, URMD-Seq is particularly well suited for epidemiological studies using a large number of specimens.

Humans↗