Presence Of Sequence Variants Research Articles

Evaluation of dental manifestations in X-linked hypophosphatemia using orthopantomography.

X-linked hypophosphatemia (XLH) is the most common inherited form of rickets. The presence of sequence variations in the phosphate regulating endopeptidase homolog X-linked (PHEX) gene is associated with increased production of fibroblast growth factor 23 (FGF23). This results in renal phosphate wasting and impaired skeletal mineralization. Spontaneous dental abscesses, caused by endodontic infections resulting from hypomineralization of dentin, are a known dental complication of XLH. There is no objective method to evaluate the severity of dentin dysplasia. The purpose of this study was to develop a quantitative method to evaluate dentin dysplasia using orthopantomography that would allow the values in patients with XLH to be compared with the values in healthy participants of the same age. The severity of dentin dysplasia was analyzed by measuring the pulp cavity area of the tooth using orthopantomographic images. The teeth analyzed were mandibular second primary molars and mandibular first permanent molars with complete root formation. Teeth with dental caries, restorations, or root resorption were excluded. This retrospective observational study included a total of 200 images of healthy participants (aged 2-15 years) divided into five age groups and 42 images of 17 patients with XLH. There was a significant tendency for the pulp cavity area to decrease with increasing age in primary and permanent teeth. The pulp chambers of patients with XLH were larger than those of healthy participants in primary and permanent teeth. We have established a method of using orthopantomography for quantitative assessment of dentin dysplasia in XLH from the primary dentition to the permanent dentition. Evaluating the severity of dentin hypomineralization by this method is useful in the diagnosis of the dental manifestations of XLH. Early diagnosis of XLH enables oral management and leads to prevention of dental abscesses.

Allele detection using k-mer-based sequencing error profiles.

For genotype and haplotype inference, typically, sequencing reads aligned to a reference genome are used. The alignments identify the genomic origin of the reads and help to infer the absence or presence of sequence variants in the genome. Since long sequencing reads often come with high rates of systematic sequencing errors, single nucleotides in the reads are not always correctly aligned to the reference genome, which can thus lead to wrong conclusions about the allele carried by a sequencing read at the variant site. Thus, allele detection is not a trivial task, especially for single-nucleotide polymorphisms and indels. To learn the characteristics of sequencing errors, we introduce a method to create an error model in non-variant regions of the genome. This information is later used to distinguish sequencing errors from alternative alleles in variant regions. We show that our method, k-merald, improves allele detection accuracy leading to better genotyping performance as compared to the existing WhatsHap implementation using edit-distance-basedallele detection, with a decrease of 18% and 24% in error ratefor high-coverage Oxford Nanopore and PacBio CLR sequencing reads for sample HG002, respectively. We additionally observed a prominent improvement in genotyping performance for sequencing data with low coverage. For 3 coverage Oxford Nanopore sequencing data, the genotyping error rate reduced from 34% to 31%, corresponding to a 9% decrease. https://github.com/whatshap/whatshap.

Sequence variations, flanking region mutations, and allele frequency at 31 autosomal STRs in the central Indian population by next generation sequencing (NGS)

Capillary electrophoresis-based analysis does not reflect the exact allele number variation at the STR loci due to the non-availability of the data on sequence variation in the repeat region and the SNPs in flanking regions. Herein, this study reports the length-based and sequence-based allelic data of 138 central Indian individuals at 31 autosomal STR loci by NGS. The sequence data at each allele was compared to the reference hg19 sequence. The length-based allelic results were found in concordance with the CE-based results. 20 out of 31 autosomal STR loci showed an increase in the number of alleles by the presence of sequence variation and/or SNPs in the flanking regions. The highest gain in the heterozygosity and allele numbers was observed in D5S2800, D1S1656, D16S539, D5S818, and vWA. rs25768 (A/G) at D5S818 was found to be the most frequent SNP in the studied population. Allele no. 15 of D3S1358, allele no. 19 of D2S1338, and allele no. 22 of D12S391 showed 5 isoalleles each with the same size and with different intervening sequences. Length-based determination of the alleles showed Penta E to be the most useful marker in the central Indian population among 31 STRs studied; however, sequence-based analysis advocated D2S1338 to be the most useful marker in terms of various forensic parameters. Population genetics analysis showed a shared genetic ancestry of the studied population with other Indian populations. This first-ever study to the best of our knowledge on sequence-based STR analysis in the central Indian population is expected to prove the use of NGS in forensic case-work and in forensic DNA laboratories.

An unusually high frequency of SCAD deficiency caused by two pathogenic variants in the ACADS gene and its relationship to the ethnic structure in Slovakia

BackgroundShort-chain acyl-CoA dehydrogenase deficiency (SCADD) represents a rare autosomal recessive inborn metabolic disorder of mitochondrial β-oxidation of monocarboxylic acids. Clinical symptoms can vary from a severe life-threatening condition to an asymptomatic state, reported in the majority of cases. Since the expansion of newborn screenings, more than three hundred probands were admitted for molecular-genetic analysis, most selected because of elevated values of C4-acylcarnitine detected in newborn screenings in Slovakia. Searching for the principal genomic changes led us to the selection of sixty-two patients in whom the presence of sequence variants in the ACADS gene was analysed and correlated with the available biochemical and clinical data.MethodsBiochemical and molecular genetic tests were performed. Acylcarnitine profiles focused on an elevated level of C4-acylcarnitine, which was analysed via tandem mass spectrometry. Urinary organic acids, specifically a quantity of ethylmalonic acid, were determined by gas chromatography/mass spectrometry. The entire coding region of the ACADS gene was sequenced. A low-cost restriction fragment length polymorphism of PCR amplified fragments analysis (PCR-RFLP) of pathogenic variants was introduced and implemented for the molecular-genetic algorithm appropriate for the Slovak population.ResultsOur molecular genetic study was performed on sixty-two patients with a pathological biochemical pattern related to short-chain acyl-CoA dehydrogenase deficiency. In this cohort, we discovered a high occurrence of two rare pathogenic variants—the deletion c.310_312delGAG and the substitution c.1138C>T, with allelic frequencies of 64% and 31%, respectively. Up to 86% of investigated individuals belong to the Roma ethnic group.ConclusionsAnalogous to other countries, SCADD is not included in the newborn screening programme. Based on the exceeded levels of the specific biomarker C4-acylcarnitine as well as ethylmalonic acid, we revealed a high prevalence of short-chain acyl-CoA dehydrogenase deficiency cases, confirmed by the findings of two rare pathogenic variants. A deletion c.310_312delGAG and c.1138C > T substitution in the ACADS gene appear with a high frequency in the Roma ethnic group of Slovakia. Due to the uncertainty of the pathogenicity and clinical consequences, it is important to follow up the morbidity and mortality in these patients over time and evaluate SCADD in relation to clinical outcomes and preventive healthcare recommendations.

Viral evolution in HLA-B27-restricted CTL epitopes in human immunodeficiency virus type 1-infected individuals.

The HLA-B27 allele is over-represented among human immunodeficiency virus type 1-infected long-term non-progressors. In these patients, strong CTL responses targeting HLA-B27-restricted viral epitopes have been associated with long-term asymptomatic survival. Indeed, loss of control of viraemia in HLA-B27 patients has been associated with CTL escape at position 264 in the immunodominant KK10 epitope. This CTL escape mutation in the viral Gag protein has been associated with severe viral attenuation and may require the presence of compensatory mutations before emerging. Here, we studied sequence evolution within HLA-B27-restricted CTL epitopes in the viral Gag protein during the course of infection of seven HLA-B27-positive patients. Longitudinal gag sequences obtained at different time points around the time of AIDS diagnosis were obtained and analysed for the presence of mutations in epitopes restricted by HLA-B27, and for potential compensatory mutations. Sequence variations were observed in the HLA-B27-restricted CTL epitopes IK9 and DR11, and the immunodominant KK10 epitope. However, the presence of sequence variations in the HLA-B27-restricted CTL epitopes could not be associated with an increase in viraemia in the majority of the patients studied. Furthermore, we observed low genetic diversity in the gag region of the viral variants throughout the course of infection, which is indicative of low viral replication and corresponds to the low viral load observed in the HLA-B27-positive patients. These data indicated that control of viral replication can be maintained in HLA-B27-positive patients despite the emergence of viral mutations in HLA-B27-restricted epitopes.

Evaluation of Sample Disruption Techniques for High Throughput Extraction of Subcellular Organelles

Modern mass spectrometers coupled with high resolution separation strategies have enabled the quantification of thousands of proteins from minute samples. However, the large dynamic range in protein abundances, the presence of sequence variants and post‐translational modifications often require that subcellular fractionation strategies be performed in order to achieve the necessary sequence coverage and signal intensity to elucidate statistically significant changes in protein expression. Subcellular fractionation enables the organelle constituents to be separated prior to downstream enzyme digestion and proteomic analysis to increase the detection of proteins of lower abundance thus increasing proteome coverage. Subcellular fractionation encompasses at least two steps; sample disruption (homogenization) and a fractionation procedure. While many organelle fractionation procedures have been described, including density centrifugation, there is no single technique that has been demonstrated to produce an ideal homogenate containing a suspension of separated intact organelles. Here we evaluate the use of three common homogenizer technologies, dounce, rotor‐stator and bead milling for the disruption of tissues for the purpose of isolating commonly analyzed organelles, including nuclei, plasma membrane, mitochondria, endoplasmic reticulum and cytosol. Mouse brain, liver and heart tissues are processed using increasing degrees of disruption forces then homogenates were separated by density centrifugation and analyzed by microscopy, western blotting and bottom up proteomics to evaluate the degree of organelle enrichment.

Abstract 1518: A new multiplex genotyping assay using PNA clamping-assisted fluorescence melting curve analysis

Abstract Recent studies on molecular mechanisms of anti-EGFR therapies revealed importance of mutation screening and genotyping of multiple target oncogenes. For example, KRAS mutations have been associated with poor responsiveness to anti-EGFR therapies. Determining the KRAS status of a newly diagnosed cancer patient prior to initiating anti-EGFR therapy would be required in selecting effective therapeutics among tyrosine kinase inhibitor and monoclonal antibody therapy. Peptide nucleic acid (PNA) is an artificially synthesized polymer. The negatively charged deoxyribose phosphate backbone of DNA is replaced by an electroneutral peptide-like backbone consisting of N-(2-aminoethyl) glycine units directly linked to the nucleotide bases. Complementary PNA/DNA complex has stronger binding affinity than complementary DNA/DNA complex. A PNA probe has higher specificity and mismatch discrimination towards its target DNA than a DNA probe. Furthermore, it shows a remarkable biological stability to enzymatic degradation. PNA is not recognized by DNA polymerase so it cannot be used as a primer. PNAClamp™ technique is the PNA-based PCR clamping that selectively amplifies only the target (mutated) DNA sequence as a minor portion in the mixture with the major non-target (wild type) DNA sequences. Therefore, PNAClamp technique provides better limit of detection than conventional PCR method. PANA S-Melting™ (PNA probe-based fluorescence melting curve analysis) based on change in fluorescent signal as a sample thermally denatured (melting temperature shift). This is a powerful tool for mutation detection (screening and genotyping) by a single probe. It can distinguish multiple sequence variants adjacent to each other on a small target region. We developed a new technique, which combines two techniques; PNAClamp and PNA probe-based fluorescence melting curve analysis. This new PNAClamp-assisted melting curve method can discriminate a sequence variant from a wild-type sequence with a relatively large Tm difference. Therefore, it could easily detect presence of sequence variation without an additional data analysis process. This technique can be performed in any real-time PCR machine, which has melting curve analysis function. We tested a new multiplex genotyping assay of KRAS gene mutation using this combined method in lung cancer cell line samples. This new assay could detect a total of seven sequence variants (6 genotypes of codon 12 and 1 genotype of codon 13) in a single closed reaction tube using three different fluorescent dyes. The results showed that 0.5 % mutations were detected using this multiplexing assay system. This new multiplex genotyping method offers a cost-effective and highly sensitive mutation genotyping method that can be used in various clinical areas including personalized medicine. Citation Format: Yongtae Kim, Jin W. Kim, Sung-Kee Kim, Goon Ho Joe. A new multiplex genotyping assay using PNA clamping-assisted fluorescence melting curve analysis. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1518. doi:10.1158/1538-7445.AM2014-1518

Nitrogen-metabolism related genes in barley - haplotype diversity, linkage mapping and associations with malting and kernel quality parameters

BackgroundSeveral studies report about intra-specific trait variation of nitrogen-metabolism related traits, such as N(itrogen)-use efficiency, protein content, N-storage and remobilization in barley and related grass species. The goal of this study was to assess the intra-specific genetic diversity present in primary N-metabolism genes of barley and to investigate the associations of the detected haplotype diversity with malting and kernel quality related traits.ResultsPartial sequences of five genes related to N-metabolism in barley (Hordeum vulgare L.) were obtained, i.e. nitrate reductase 1, glutamine synthetase 2, ferredoxin-dependent glutamate synthase, aspartate aminotransferase and asparaginase. Two to five haplotypes in each gene were discovered in a set of 190 various varieties. The development of 33 SNP markers allowed the genotyping of all these barley varieties consisting of spring and winter types. Furthermore, these markers could be mapped in several doubled haploid populations. Cluster analysis based on haplotypes revealed a more uniform pattern of the spring barleys as compared to the winter barleys. Based on linear model approaches associations to several malting and kernel quality traits including soluble N and protein were identified.ConclusionsA study was conducted to investigate the presence of sequence variation of several genes related to the primary N-metabolism in barley. The detected diversity could be related to particular phenotypic traits. Specific differences between spring and winter barleys most likely reflect different breeding aims. The developed markers can be used as tool for further genetic studies and marker-assisted selection during breeding of barley.

Genetic variants in miR-146a, miR-149, miR-196a2, miR-499 and their influence on relative expression in lung cancers

The presence of sequence variants in miRNA genes may influence their processing, expression and binding to target mRNAs. Since single miRNA can have a large number of potential mRNA targets, even minor variations in its expression can have influences on hundreds of putative mRNAs. Here, we evaluated 101 paired samples (cancer and normal tissues) from non-small cell lung carcinoma (NSCLC) patients to study the genotype distribution of single nucleotide polymorphisms (SNPs) in miR-146a (rs2910164 C-G), miR-149 (rs2292832 C-T), miR-196a2 (rs11614913 C-T) and miR-499 (rs3746444 G-A) and their influence on the expression of respective miRNAs. Relative expression of miR-146a, miR-149 and miR-499 were comparable in NSCLC and in paired control tissues. On the contrary, we clearly detected a significant increase (p<0.001) of miR-196a2 expression in NSCLC. In particular we found a significant association between miR-196a2 CC genotype and high expression, whereas TT geno-type showed a very low expression in comparison to both CT (p<0.005) and CC patients (p<0.01). We did not find any association between miR-149, miR-196a2 and miR-499 genotype and risk of NSCLC. Conversely, CG genotype of miR-146a appeared associated to an increased risk for NSCLC (p=0.042 and 1.77 OR). Our results seem to demonstrate that sequence variants of miR-196a2 can have an influence on its expression, while miR-146a can have a role in increasing the risk of NSCLC.

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

High-volume sequencing of DNA and RNA is now within reach of any research laboratory and is quickly becoming established as a key research tool. In many workflows, each of the short sequences ("reads") resulting from a sequencing run are first "mapped" (aligned) to a reference sequence to infer the read from which the genomic location derived, a challenging task because of the high data volumes and often large genomes. Existing read mapping software excel in either speed (e.g., BWA, Bowtie, ELAND) or sensitivity (e.g., Novoalign), but not in both. In addition, performance often deteriorates in the presence of sequence variation, particularly so for short insertions and deletions (indels). Here, we present a read mapper, Stampy, which uses a hybrid mapping algorithm and a detailed statistical model to achieve both speed and sensitivity, particularly when reads include sequence variation. This results in a higher useable sequence yield and improved accuracy compared to that of existing software.

The Impact of CpG Island on Defining Transcriptional Activation of the Mouse L1 Retrotransposable Elements

BackgroundL1 retrotransposable elements are potent insertional mutagens responsible for the generation of genomic variation and diversification of mammalian genomes, but reliable estimates of the numbers of actively transposing L1 elements are mostly nonexistent. While the human and mouse genomes contain comparable numbers of L1 elements, several phylogenetic and L1Xplore analyses in the mouse genome suggest that 1,500–3,000 active L1 elements currently exist and that they are still expanding in the genome. Conversely, the human genome contains only 150 active L1 elements. In addition, there is a discrepancy among the nature and number of mouse L1 elements in L1Xplore and the mouse genome browser at the UCSC and in the literature. To date, the reason why a high copy number of active L1 elements exist in the mouse genome but not in the human genome is unknown, as are the potential mechanisms that are responsible for transcriptional activation of mouse L1 elements.Methodology/Principal FindingsWe analyzed the promoter sequences of the 1,501 potentially active mouse L1 elements retrieved from the GenBank and L1Xplore databases and evaluated their transcription factors binding sites and CpG content. To this end, we found that a substantial number of mouse L1 elements contain altered transcription factor YY1 binding sites on their promoter sequences that are required for transcriptional initiation, suggesting that only a half of L1 elements are capable of being transcriptionally active. Furthermore, we present experimental evidence that previously unreported CpG islands exist in the promoters of the most active TF family of mouse L1 elements. The presence of sequence variations and polymorphisms in CpG islands of L1 promoters that arise from transition mutations indicates that CpG methylation could play a significant role in determining the activity of L1 elements in the mouse genome.ConclusionsA comprehensive analysis of mouse L1 promoters suggests that the number of transcriptionally active elements is significantly lower than the total number of full-length copies from the three active mouse L1 families. Like human L1 elements, the CpG islands and potentially the transcription factor YY1 binding sites are likely to be required for transcriptional initiation of mouse L1 elements.

The associations of sequence variants in DNA-repair and cell-cycle genes with cancer risk: genotype–phenotype correlations

DNA-repair systems maintain the integrity of the human genome, and cell-cycle checkpoints are a critical component of the cellular response to DNA damage. Thus the presence of sequence variants in genes involved in these pathways that modulate their activity might have an impact on cancer risk. Many molecular epidemiological studies have investigated the association between sequence variants, particularly SNPs (single nucleotide polymorphisms), and cancer risk. For instance, ATM (ataxia telangiectasia mutated) SNPs have been associated with increased risk of breast, prostate, leukaemia, colon and early-onset lung cancer, and the intron 3 16-bp repeat in TP53 (tumour protein 53) is associated with an increased risk of lung cancer. In contrast, the variant allele of the rare CHEK2 (checkpoint kinase 2 checkpoint homologue) missense variant (accession number rs17879961) was significantly associated with a lower incidence of lung and upper aerodigestive cancers. For some sequence variants, a strong gene-environment interaction has also been noted. For instance, a greater absolute risk reduction of lung and upper aerodigestive cancers in smokers than in non-smokers carrying the I157T CHEK2 variant has been observed, as has an interaction between TP53 intron 3 16-bp repeats and multiple X-ray exposures on lung cancer risk. The challenge now is to understand the molecular mechanisms underlying these associations.

Cloning of caninemyocilincDNA and molecular analysis of themyocilingene in Shiba Inu dogs

To identify canine myocilin cDNA and compare its sequence in glaucomatous and nonglaucomatous Shiba Inu dogs with closed and open iridocorneal angles (ICAs). Total RNA was extracted from the ciliary body of the eyes of a healthy Beagle, and the canine myocilin gene was cloned and sequenced. Of the Shiba Inu dogs tested, five were glaucomatous with closed ICA, three were nonglaucomatous with open ICA, and two were nonglaucomatous with closed ICA. The genomic DNA of these dogs was extracted from peripheral blood leukocytes. The exons of the canine myocilin gene were amplified using the polymerase chain reaction (PCR), and sequenced. The frequency of mutation in canine myocilin DNA was verified in these dogs by using the myocilin cDNA of a Beagle. The canine myocilin cDNA was 1452 bp long and contained the entire open reading frame encoding 483 amino acids. A leucine zipper-like motif and olfactomedin-like domain were conserved in the amino acid residues. The presence of sequence variants in the genomic DNA of Shiba Inu dogs was independent of the occurrence of glaucoma and ICA grading. Myocilin RNA was detected in the ciliary body and trabecular meshwork (TM) of a Beagle. The myocilin sequence of Shiba Inu dogs suggests that myocilin mutations are unlikely to play a significant role in the pathogenesis of primary closed-angle glaucoma in this breed. However, several mutations in the myocilin gene in exon 1 of Shiba Inu dogs may predispose them to an obstruction in the anterior aqueous outflow.

Masking selected sequence variation by incorporating mismatches into melting analysis probes

Hybridization probe melting analysis can be complicated by the presence of sequence variation (benign polymorphisms or other mutations) near the targeted mutation. We investigated the use of "masking" probes to differentiate alleles with similar probe melting temperatures. Selected sequence variation was masked by incorporating mismatches (deletion, unmatched nucleotide, or universal base) into hybridization probes at the polymorphic location. Such masking probes create a probe/target mismatch with all possible alleles at the selected polymorphic location. Any allele with additional variation at another site is identified by a lower probe melting temperature than alleles that vary only at the masked position. This "masking technique" was applied to RET protooncogene and HPA6 mutation detection using unlabeled hybridization probes, a saturating dsDNA dye, and high-resolution melting analysis. Masking probes clearly distinguished all targeted mutations from polymorphisms when at least 1 base pair (bp) separated the mutation from the masked variation. We were able to mask polymorphisms immediately adjacent to mutations, except in certain cases, such as those involving single-base deletion probes when both adjacent positions had the same polymorphic nucleotides. The masking probes can also localize mutations to specific codons or nucleotide positions. Masking probes can simplify melting analysis of complex regions and eliminate the need for sequencing.

Sequence variation and the transcriptional activity of the upstream regulatory region in human papillomavirus 16 E7 variants in cervical cancer of Korean women

In this study, we investigated the sequence variation and different transcriptional activities of the upstream regulatory region (URR) in HPV 16 E7 variants in cervical cancer tissue from Korean women. Using PCR-directed sequencing, the presence of sequence variations in URRs were analyzed and the sites of sequence variation were matched with the known transcriptional factor binding site (TFBS) in 26 HPV 16 E7 variants, 21 cases with A647G (KE7-1, high oncogenic potential) and 5 cases with T732C (KE7-2, low oncogenic potential). In addition, we determined the transcriptional activity of URR in a HPV 16 prototype, and in 4 cases of HPV 16 E7 variants, by using the functional chloramphenicol acetyl transferase (CAT) assay. The 26 HPV 16 E7 variants showed more than 11 sites of sequence variation in the URR. Ten sites of sequence variation were located in the known TFBS and the distribution of sequence variations in the URR showed clear differences between KE7-1 and KE7-2. The sequence variations T7781C and C7786T were matched with YY1 binding sites, G7193T and C7689A were matched with TEF1 binding sites, and C7394T and C7395T were matched with GRE binding sites. The other sequence variations, which were matched with the TFBS, were A7485C, G7489A, T7743G and G7842A. The URR activity of KE7-1 was significantly lower than that of the HPV 16 prototype, whilst KE7-2 was similar. Taken together with the results of the transcriptional activities of KE7-1 and KE7-2, our results suggest that the functional activity and sequence variations of HPV 16 URR may not be related to the oncogenic potential of HPV 16 E7 variants.

ATM sequence variants are predictive of adverse radiotherapy response among patients treated for prostate cancer

To examine whether the presence of sequence variants in the ATM (mutated in ataxia-telangiectasia) gene is predictive for the development of radiation-induced adverse responses resulting from (125)I prostate brachytherapy for early-stage prostate cancer. Thirty-seven patients with a minimum of 1-year follow-up who underwent (125)I prostate brachytherapy of early-stage prostate cancer were screened for DNA sequence variations in all 62 coding exons of the ATM gene using denaturing high-performance liquid chromatography. The clinical course and postimplant dosimetry for each genetically characterized patient were obtained from a database of 2,020 patients implanted at Mount Sinai Hospital after 1990. Twenty-one ATM sequence alterations located within exons, or in short intronic regions flanking each exon, were found in 16 of the 37 patients screened. For this group, 10 of 16 (63%) exhibited at least one form of adverse response. In contrast, of the 21 patients who did not harbor an ATM sequence variation, only 3 of 21 (14%) manifested radiation-induced adverse responses (p = 0.005). Nine of the patients with sequence alterations specifically possessed missense mutations, which encode for amino acid substitutions and are therefore more likely to possess functional importance. For this group, 7 of 9 (78%) exhibited at least one form of adverse response. In contrast, of the 28 patients who did not have a missense alteration, only 6 of 28 (21%) manifested any form of adverse response to the radiotherapy (p = 0.004). Of the patients with missense variants, 5 of 9 (56%) exhibited late rectal bleeding vs. 1 of 28 (4%) without such alterations (p = 0.002). Of those patients who were at risk for developing erectile dysfunction, 5 of 8 (63%) patients with missense mutations developed prospectively evaluated erectile dysfunction as opposed to 2 of 20 (10%) without these sequence alterations (p = 0.009). Possession of sequence variants in the ATM gene, particularly those that encode for an amino acid substitution, is predictive for the development of adverse radiotherapy responses among patients treated with (125)I prostate brachytherapy.

Atm sequence variants are predictive of adverse radiotherapy response among patients treated for prostate cancer

Atm sequence variants are predictive of adverse radiotherapy response among patients treated for prostate cancer

HPV-16 E2 gene disruption and sequence variation in CIN 3 lesions and invasive squamous cell carcinomas of the cervix: relation to numerical chromosome abnormalities

Aim—To test the hypothesis that, because the human papillomavirus (HPV) E2 protein represses viral early gene transcription, E2 gene sequence variation or disruption could play a part in the induction...

Molecular Analysis of Single B Cells From T-Cell–Rich B-Cell Lymphoma Shows the Derivation of the Tumor Cells From Mutating Germinal Center B Cells and Exemplifies Means by Which Immunoglobulin Genes Are Modified in Germinal Center B Cells

T-cell–rich B-cell lymphoma (TCRBCL) belongs to the group of diffuse large cell lymphomas (DLL). It is characterized by a small number of tumor B cells among a major population of nonmalignant polyclonal T cells. To identify the developmental stage of the tumor progenitor cells, we micromanipulated the putative neoplastic large CD20+ cells from TCRBCLs and amplified and sequenced immunoglobulin (Ig) V gene rearrangements from individual cells. In six cases, clonal Ig heavy, as well as light chain, gene rearrangements were amplified from the isolated B cells. All six cases harbored somatically mutated V gene rearrangements with an average mutation frequency of 15.5% for heavy (VH) and 5.9% for light (VL) chains and intraclonal diversity based on somatic mutation. These findings identify germinal center (GC) B cells as the precursors of the transformed B cells in TCRBCL. The study also exemplifies various means how Ig gene rearrangements can be modified by GC B cells or their malignant counterparts in TCRBCL: In one case, the tumor precursor may have switched from κ to λ light chain expression after acquiring a crippling mutation within the initially functional κ light chain gene. In another case, the tumor cells harbor two in-frame VH gene rearrangements, one of which was rendered nonfunctional by somatic mutation. Either the tumor cell precursor entered the GC with two potentially functional in-frame rearrangements or the second VHDHJHrearrangement occurred in the GC after the initial in-frame rearrangement was inactivated by somatic mutation. Finally, in each of the six cases, at least one cell contained two (or more) copies of a clonal Ig gene rearrangement with sequence variations between these copies. The presence of sequence variants for V region genes within single B cells has so far not been observed in any other normal or transformed B lymphocyte. Fluorescence in situ hybridization (FISH) points to a generalized polyploidy of the tumor cells.

Nucleotide sequence of the rice cytochrome ⨍ gene and the presence of sequence variation near this gene

The rice ( Oryza saliva L. var. Labelle) chloroplast (cp) gene encoding cytochrome ⨍ has been isolated and sequenced. The coding region of this rice gene displays 95.1%, 85.3% and 85.2% nucleotide sequence homology with that of wheat, pea and spinach, respectively. To examine the cpDNA sequence variation in rice, cpDNA from Labelle and its parents, Belle Patna and Dawn was compared. Using the cytochrome ⨍ gene as the probe for hybridization, we found several differences in the size and number of restriction fragments in the cp genome of three rice varieties. An additional restriction fragment found in the Belle Patna cp suggests that this cp genome is either heterogeneous or contains two copies of cytochrome ⨍ gene per cpDNA.