Common DNA Sequence Research Articles

Meta-analysis of 32 genome-wide linkage studies of schizophrenia.

A genome scan meta-analysis (GSMA) was carried out on 32 independent genome-wide linkage scan analyses that included 3255 pedigrees with 7413 genotyped cases affected with schizophrenia (SCZ) or related disorders. The primary GSMA divided the autosomes into 120 bins, rank-ordered the bins within each study according to the most positive linkage result in each bin, summed these ranks (weighted for study size) for each bin across studies and determined the empirical probability of a given summed rank (P(SR)) by simulation. Suggestive evidence for linkage was observed in two single bins, on chromosomes 5q (142-168 Mb) and 2q (103-134 Mb). Genome-wide evidence for linkage was detected on chromosome 2q (119-152 Mb) when bin boundaries were shifted to the middle of the previous bins. The primary analysis met empirical criteria for 'aggregate' genome-wide significance, indicating that some or all of 10 bins are likely to contain loci linked to SCZ, including regions of chromosomes 1, 2q, 3q, 4q, 5q, 8p and 10q. In a secondary analysis of 22 studies of European-ancestry samples, suggestive evidence for linkage was observed on chromosome 8p (16-33 Mb). Although the newer genome-wide association methodology has greater power to detect weak associations to single common DNA sequence variants, linkage analysis can detect diverse genetic effects that segregate in families, including multiple rare variants within one locus or several weakly associated loci in the same region. Therefore, the regions supported by this meta-analysis deserve close attention in future studies.

Epigenetics and Obesity

Common DNA sequence variants inadequately explain variability in fat mass among individuals. Abnormal body weights are characteristic of specific imprinted-gene disorders. However, the relevance of imprinted genes to our understanding of obesity among the general population is uncertain. Hitherto unidentified imprinted genes and epigenetic mosaicism are two of the challenges for this emerging field of epigenetics. Subtle epigenetic differences in imprinted genes and gene networks are likely to be present among cells, tissues and individuals. In order to advance obesity research it will be necessary to use genome-wide, next-generation sequencing approaches that allow the detection of such epigenetic differences.

Genome scanning and cardiovascular disease

At the end of 2007, Science recognised human genetic variation as the “breakthrough of the year”.1 Beginning in April last year and extending through the current year, major advances have...

Different evolutionary trails in the related genomes Cricetus cricetus and Peromyscus eremicus (Rodentia, Cricetidae) uncovered by orthologous satellite DNA repositioning

Constitutive heterochromatin comprises a substantial fraction of the eukaryotic genomes and is mainly composed of tandemly arrayed satellite DNAs (satDNA). These repetitive sequences represent a very dynamic and fast evolving component of genomes. In the present work we report the isolation of Cricetus cricetus (CCR, Cricetidae, Rodentia) centromeric repetitive sequences from chromosome 4 (CCR4/10sat), using the laser microdissection and laser pressure catapulting procedure, followed by DOP-PCR amplification and labelling. Physical mapping by fluorescent in situ hybridisation of these sequences onto C. cricetus and another member of Cricetidae, Peromyscus eremicus, displayed quite interesting patterns. Namely, the centromeric sequences showed to be present in another C. cricetus chromosome (CCR10) besides CCR4. Moreover, these almost chromosome-specific sequences revealed to be present in the P. eremicus genome, and most interestingly, displaying a ubiquitous scattered distribution throughout this karyotype. Finally and in both species, a co-localisation of CCR4/10sat with constitutive heterochromatin was found, either by classical C-banding or C-banding sequential to in situ endonuclease restriction. The presence of these orthologous sequences in both genomes is suggestive of a phylogenetic proximity. Furthermore, the existence of common repetitive DNA sequences with a different chromosomal location foresees the occurrence of an extensive process of karyotype restructuring somehow related with intragenomic movements of these repetitive sequences during the evolutionary process of C. cricetus and P. eremicus species.

Defining the spectrum of alleles that contribute to blood lipid concentrations in humans

Recently, genome-wide genetic screening of common DNA sequence variants has proven a successful approach to identify novel genetic contributors to complex traits. This review summarizes recent genome-wide association studies for lipid phenotypes, and evaluates the next steps needed to obtain a full picture of genotype-phenotype correlation and apply these findings to inform clinical practice. So far, genome-wide association studies have defined at least 19 genomic regions that contain common DNA single nucleotide polymorphisms associated with LDL cholesterol, HDL cholesterol and/or triglycerides. Of these, eight represent novel loci in humans, whereas 11 genes have been previously implicated in lipoprotein metabolism. Many of the same loci with common variants have already been shown to lead to monogenic lipid disorders in humans and/or mice, suggesting that a spectrum of common and rare alleles at each validated locus contributes to blood lipid concentrations. At least 19 loci harbor common variations that contribute to blood lipid concentrations in humans. Larger scale genome-wide association studies should identify additional loci, and sequencing of these loci should pinpoint all relevant alleles. With a full catalog of DNA polymorphisms in hand, a panel of lipid-related variants can be studied to provide clinical risk stratification and targeting of therapeutic interventions.

Phosphatidylcholine Biosynthesis and Neuronal Differentiation

Neuronal differentiation is a complex process characterized by a halt in proliferation and extension of neurites from the cell body. Changes in gene expression mediate the metabolic redirection leading to neurite formation and function. Acceleration of membrane phospholipid synthesis is associated with neurite elongation and phosphatidylcholine (PtdCho) is the major membrane phospholipid in mammalian cells. Our results indicate that membrane biogenesis is driven by the elevated expression of a subset of lipid biosynthetic genes following retinoic acid (RA)‐induced differentiation of Neuro2A cells. The transcription of genes encoding key enzymes in the CDP‐choline pathway of phospholipid biosynthesis is stimulated, including the Chka gene for choline kinase (CK) and the Pcyt1a gene for the CTP:phosphocholine cytidylyltransferase (CCT). The promoter regions for both genes indicated common DNA sequences which are proposed to be binding sites for transcription factors (TFs) that coordinately activate expression in a RA‐dependent manner. Alteration of CK or CCT expression regulated PtdCho synthesis and neurite extension following RA treatment. These results indicate that PtdCho synthesis is important for RA‐dependent differentiation of Neuro2A cells.

Isolation of selectively amplified DNA sequences from multidrug-resistant SEWA cells.

It was determined that some common DNA sequences had been amplified in all the lines, but that the total DNA region amplified varied among lines. We compared the DM-containing AMD-resistant line to a line with homogeneously staining regions (HSR), which had been derived from it by prolonged maintenance under constant selection in AMD. With 1 probe it was found that some previously unamplified DNA sequences were amplified in the HSR-carrying line, suggesting a complex mechanism behind the transition from DM to HSR. In contrast, identical Southern blot patterns were found in the AMD-resistant line with DM and 4 subclones with different HSR, indicating that in this case the HSR arose by integration of an amplicon present in the DM (without extensive rearrangement) rather than by a second amplification event. The tentative conclusion from our experiments is that in SEWA cells MDR is accomplished by the amplification of DNA sequences. The primary amplified DNA resides in DM, which under constant selection tend to be replaced by HSR. This second step may or may not be accompanied by amplification of previously unamplified DNA sequences.

Beginning to Unravel the Common, Low-Penetrance Genetic Components Behind Colorectal Cancer by Whole-Genome Association Scans

Beginning to Unravel the Common, Low-Penetrance Genetic Components Behind Colorectal Cancer by Whole-Genome Association Scans

Risk Alleles for Multiple Sclerosis Identified by a Genomewide Study

Multiple sclerosis has a clinically significant heritable component. We conducted a genomewide association study to identify alleles associated with the risk of multiple sclerosis. We used DNA microarray technology to identify common DNA sequence variants in 931 family trios (consisting of an affected child and both parents) and tested them for association. For replication, we genotyped another 609 family trios, 2322 case subjects, and 789 control subjects and used genotyping data from two external control data sets. A joint analysis of data from 12,360 subjects was performed to estimate the overall significance and effect size of associations between alleles and the risk of multiple sclerosis. A transmission disequilibrium test of 334,923 single-nucleotide polymorphisms (SNPs) in 931 family trios revealed 49 SNPs having an association with multiple sclerosis (P<1x10(-4)); of these SNPs, 38 were selected for the second-stage analysis. A comparison between the 931 case subjects from the family trios and 2431 control subjects identified an additional nonoverlapping 32 SNPs (P<0.001). An additional 40 SNPs with less stringent P values (<0.01) were also selected, for a total of 110 SNPs for the second-stage analysis. Of these SNPs, two within the interleukin-2 receptor alpha gene (IL2RA) were strongly associated with multiple sclerosis (P=2.96x10(-8)), as were a nonsynonymous SNP in the interleukin-7 receptor alpha gene (IL7RA) (P=2.94x10(-7)) and multiple SNPs in the HLA-DRA locus (P=8.94x10(-81)). Alleles of IL2RA and IL7RA and those in the HLA locus are identified as heritable risk factors for multiple sclerosis.

A common 93-kb duplicated DNA sequence at 1q21.2 in acute lymphoblastic leukemia and Burkitt lymphoma

In three patients with acute lymphoblastic leukemia (ALL) and in another with Burkitt lymphoma (BL), conventional cytogenetics and fluorescence in situ hybridization (FISH), applied singly or in combination, showed 1q duplication in two cases of ALL with hyperdiploid karyotypes, 1q duplication resulting from an unbalanced translocation in a third case of ALL, and inv dup(1)(q) in a patient with BL. Centromeric or telomeric breakpoints and extension of the 1q duplicons varied in each case. FISH defined a minimal, common duplicated region of 93kb at band 1q21.2 corresponding to clone RP11-212K13. In this region three putative oncogenes or tumor suppressor genes have been mapped: SF3B4 (splicing factor 3b, subunit 4), OTUD7B (OTU domain containing 7B), and MTMR11 (myotubularin related protein 11). For the first time, a minimal common 1q21.2 duplicated sequence has been identified in lymphoid malignancies in a region where putative oncogenes or suppressor genes have been mapped. This finding elucidates the genomic background of ALL and BL with 1q duplication and provides the basis for molecular studies investigating which genes are involved in leukemogenesis or disease progression in these cases.

Hematopoietic gene promoters subjected to a group-combinatorial study of DNA samples: identification of a megakaryocytic selective DNA signature

Identification of common sub-sequences for a group of functionally related DNA sequences can shed light on the role of such elements in cell-specific gene expression. In the megakaryocytic lineage, no one single unique transcription factor was described as linage specific, raising the possibility that a cluster of gene promoter sequences presents a unique signature. Here, the megakaryocytic gene promoter group, which consists of both human and mouse 5′ non-coding regions, served as a case study. A methodology for group-combinatorial search has been implemented as a customized software platform. It extracts the longest common sequences for a group of related DNA sequences and allows for single gaps of varying length, as well as double- and multiple-gap sequences. The results point to common DNA sequences in a group of genes that is selectively expressed in megakaryocytes, and which does not appear in a large group of control, random and specific sequences. This suggests a role for a combination of these sequences in cell-specific gene expression in the megakaryocytic lineage. The data also point to an intrinsic cross-species difference in the organization of 5′ non-coding sequences within the mammalian genomes. This methodology may be used for the identification of regulatory sequences in other lineages.

Comparing the performance of a reversible jump Markov chain Monte Carlo algorithm for DNA sequences alignment

Assume that K independent copies are made from a common prototype DNA sequence whose length is a random variable. In this paper, the problem of aligning those copies and therefore the problem of estimating the prototype sequence that produced the copies is addressed. A hidden Markov chain is used to model the copying procedure, and a reversible jump Markov chain Monte Carlo algorithm is used to sample the parameters of the model from their posterior distribution. Using the sample obtained, the Bayesian model and the prototype sequence may be selected using the maximum a posteriori estimate. A prior distribution for the prototype DNA sequence that incorporates a correlation among neighbouring bases is also considered. In addition, an analysis of the performance of the algorithm is presented when different scenarios are taken into account.

Identification of cis- and trans-acting factors possibly modifying the risk of epimutations on chromosome 15

In the majority of patients with a chromosome 15 imprinting defect (ID) causing Prader-Willi syndrome (PWS) or Angelman syndrome (AS), the defect is a primary epimutation that occurred spontaneously in the absence of a DNA mutation. We have investigated whether common DNA sequence variants in the bipartite imprinting centre (IC) are associated with an increased susceptibility to imprinting defects. We have determined the haplotype structure of the IC and found that the two IC elements called 'PWS-SRO' and 'AS-SRO' lie on separate haplotype blocks. To identify susceptible IC sequence variants, we have used the transmission disequilibrium test. While we did not observe preferential transmission of a paternal allele or haplotype in 41 PWS-ID trios, we found a trend for preferential maternal transmission of one AS-SRO haplotype (H-AS3) in 48 AS-ID trios (P=0.058) and could identify two sequence variants in H-AS3 that are responsible for this effect. We also obtained tentative evidence that homozygosity for the 677C>T variant of the 5,10-methylenetetrahydrofolate reductase (MTHFR) gene on chromosome 1 might increase the risk of a maternal imprinting defect: the frequency of the TT genotype was significantly higher in the mothers of the AS patients with an imprinting defect than in the patients' fathers or the general population (P=0.028). Our findings suggest that women with the IC haplotype H-AS3 or homozygosity for the MTHFR 677C>T variant may have an increased risk of conceiving a child with an imprinting defect, although the absolute risk is low.

Telomere Binding Protein Taz1 Establishes Swi6 Heterochromatin Independently of RNAi at Telomeres

The telomere is a specialized heterochromatin conserved among eukaryotes. However, it remains unknown how heterochromatin protein 1 (HP1) is recruited to telomeres and how telomere heterochromatin is formed. In fission yeast, the RNAi (RNA interference)-RITS (RNA-induced initiation of transcriptional silencing) pathway initiates heterochromatin formation at the centromeres and the silent mat locus by using common DNA sequences, the dg and dh repeats, as the templates for small interfering RNA (siRNA). We found that telomeric repeats are sufficient for the establishment of Swi6 (a fission-yeast HP1 homolog) heterochromatin, and the establishment requires Taz1, a telomere binding protein of the TRF family. Additionally, Swi6 heterochromatin is established by a part of the subtelomere that contains sequences highly homologous to that of the dh repeat, and it is strikingly destabilized by the deletion of both Taz1 and RNAi-RITS. Transcripts from the telomeric dh-homologous region were specifically associated with RITS, and deletion of the telomeric dh-homologous region showed the phenotype similar to that of the rnai mutant in terms of the telomeric silencing, indicating that the RNAi-RITS pathway acts at the telomeric dh-homologous region to establish Swi6 heterochromatin. Furthermore, we found that Taz1 establishes Swi6 heterochromatin independently of the telomeric repeats and the RNAi-RITS pathway at the subtelomeres. The telomere heterochromatin is regulated by at least two factors: One is Taz1, which is telomere specific, and the other is RNAi-RITS, which is commonly used at the constitutive heterochromatin regions.

P16: Aneuploidy-screening in single cells by a rapid comparative genomic hybridization protocol for prenatal diagnostics

Constitutive heterochromatin comprises a substantial fraction of the eukaryotic genomes and is mainly composed of tandemly arrayed satellite DNAs (satDNA). These repetitive sequences represent a very dynamic and fast evolving component of genomes. In the present work we report the isolation of Cricetus cricetus (CCR, Cricetidae, Rodentia) centromeric repetitive sequences from chromosome 4 (CCR4/10sat), using the laser microdissection and laser pressure catapulting procedure, followed by DOP-PCR amplification and labelling. Physical mapping by fluorescent in situ hybridisation of these sequences onto C. cricetus and another member of Cricetidae, Peromyscus eremicus, displayed quite interesting patterns. Namely, the centromeric sequences showed to be present in another C. cricetus chromosome (CCR10) besides CCR4. Moreover, these almost chromosome-specific sequences revealed to be present in the P. eremicus genome, and most interestingly, displaying a ubiquitous scattered distribution throughout this karyotype. Finally and in both species, a co-localisation of CCR4/10sat with constitutive heterochromatin was found, either by classical C-banding or C-banding sequential to in situ endonuclease restriction.The presence of these orthologous sequences in both genomes is suggestive of a phylogenetic proximity. Furthermore, the existence of common repetitive DNA sequences with a different chromosomal location foresees the occurrence of an extensive process of karyotype restructuring somehow related with intragenomic movements of these repetitive sequences during the evolutionary process of C. cricetus and P. eremicus species.

Genomics: HapMap Complete

Vol. 113, No. 10 EnvironewsOpen AccessGenomics: HapMap Complete Charles W. Schmidt Charles W. Schmidt Search for more papers by this author Published:1 October 2005https://doi.org/10.1289/ehp.113-a662aAboutSectionsPDF ToolsDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InReddit The International HapMap Project, a consortium of researchers and funding agencies from the United States, Japan, China, Nigeria, Canada, and the United Kingdom, is set to release a dramatically enhanced version of its haplotype map. The newly revised HapMap will be formally introduced on 26 October 2005 at the annual meeting of the American Society of Human Genetics in Salt Lake City. This information will provide researchers with an effective shortcut to map the genes contributing to particular diseases and drug responses.The HapMap currently characterizes a total of 4 million common DNA sequence variants known as single-nucleotide polymorphisms (SNPs). With the HapMap, scientists are better able to investigate the genetic components of many complex disorders, such as asthma, cancer, and obesity. Mark Daly, an associate member of the Broad Institute, a research collaboration of universities, research centers, and hospitals in Cambridge, Massachusetts, says the HapMap shows where common SNPs are located on human DNA, and how they are distributed among populations in different parts of the world. “The HapMap allows us to accelerate our understanding of genetic variation and its relationship to disease,” he says.Most SNPs are inherited in blocks, or haplotypes, on the chromosome. Each haplotype typically carries “tag” SNPs that characterize the haplotype as a whole and thus can be used to predict the identity of the other SNPs in the same block. For example, if researchers found that a certain tag SNP showed up consistently in studies of bipolar disorder, that tag could provide some indication of the other nearby SNPs on the chromosome—SNPs that may act in concert to exert some effect on the individual phenotype. Researchers can then look more closely at those neighboring SNPs to see whether and how they contribute to a given disease. The HapMap project has identified 250,000–400,000 such tag SNPs.Phase I of the project, which was completed in March 2005, characterized 1 million SNPs in the genomes of 269 individuals from four sampled populations: the Yoruba people of Nigeria, Han Chinese from Beijing, Japanese people from Tokyo, and a group in Utah with ancestry from Western and Northern Europe.In Phase II, the HapMap increased the SNP density characterization in these populations to 4 million. According to Daly, this expanded number encompasses the vast majority of common SNPs thought to exist in human beings.Lisa Brooks, program director of the Genetic Variation Program at the National Human Genome Research Institute, says that researchers will seek to validate the current HapMap’s findings in additional populations, including African Americans, Mexican Americans, and others. “Phase II has given us a better genomewide HapMap,” she explains. “This is a wonderful resource for mapping genes affecting complex diseases.”FiguresReferencesRelatedDetails Vol. 113, No. 10 October 2005Metrics About Article Metrics Publication History Originally published1 October 2005Published in print1 October 2005 Financial disclosuresPDF download License information EHP is an open-access journal published with support from the National Institute of Environmental Health Sciences, National Institutes of Health. All content is public domain unless otherwise noted. Note to readers with disabilities EHP strives to ensure that all journal content is accessible to all readers. However, some figures and Supplemental Material published in EHP articles may not conform to 508 standards due to the complexity of the information being presented. If you need assistance accessing journal content, please contact [email protected]. Our staff will work with you to assess and meet your accessibility needs within 3 working days.

Characterization of transgene integration pattern in F4 hGH-transgenic common carp (Cyprinus carpio L.)

The integration pattern and adjacent host sequences of the inserted pMThGH-transgene in the F4 hGH-transgenic common carp were extensively studied. Here we show that each F4 transgenic fish contained about 200 copies of the pMThGH-transgene and the transgenes were integrated into the host genome generally with concatemers in a head-to-tail arrangement at 4-5 insertion sites. By using a method of plasmid rescue, four hundred copies of transgenes from two individuals of F4 transgenic fish, A and B, were recovered and clarified into 6 classes. All classes of recovered transgenes contained either complete or partial pMThGH sequences. The class I, which comprised 83% and 84.5% respectively of the recovered transgene copies from fish A and B, had maintained the original configuration, indicating that most transgenes were faithfully inherited during the four generations of reproduction. The other five classes were different from the original configuration in both molecular weight and restriction map, indicating that a few transgenes had undergone mutation, rearrangement or deletion during integration and germline transmission. In the five types of aberrant transgenes, three flanking sequences of the host genome were analyzed. These sequences were common carp b-actin gene, common carp DNA sequences homologous to mouse phosphoglycerate kinase-1 and human epidermal keratin 14, respectively.

Locked Nucleic Acid-Enhanced Detection of 1100delC*CHEK2 Germ-Line Mutation in Spanish Patients with Hematologic Malignancies

The prediction that there might be common DNA sequence variants that confer a small but appreciably enhanced risk of cancer has been validated with the discovery of the germ-line mutation 1100delC in the cell cycle checkpoint kinase gene ( CHEK2 ; OMIM 604373) (1)(2). CHEK2 is located on chromosome 22q and encodes the human ortholog of yeast Cds1 and Rad53, which are G2-checkpoint kinases (3). CHEK2 is a protein kinase activated in response to DNA damage involved in cell-cycle arrest. It serves as a link in the ATM-CHEK2-CDC25A-CDK2 pathway that checks genomic integrity in response to DNA damage (4). The 1100delC mutation in exon 10 abolishes the kinase function of CHEK2 (5) and has been reported in patients with Li–Fraumeni syndrome in the United States and in Finnish families with a cancer phenotype suggestive of Li–Fraumeni syndrome, including breast cancer (5). There have been recent reports of a higher incidence of the 1100delC mutated allele in patients with a family history of breast cancer who are not carriers of BRCA1 (OMIM 113705) or BRCA2 (OMIM 600185) mutations, compared with healthy controls (4.2% and 5.5% in breast cancer cases vs 1.4% and 1.1% in controls, respectively) (1)(6). The presence of the mutated allele approximately doubles the breast cancer risk in women and increases it 10-fold in men (1). It has also been reported that 4.8% of individuals with familial prostate cancer are carriers of distinct CHEK2 germ-line mutations (7). These mutations may contribute to prostate cancer risk, highlighting the importance of the integrity of DNA damage-signaling pathways in the development of prostate cancer. The few reports for patients with hematologic malignancies have been concerned mainly with CHEK2 somatic mutations (8)(9)(10). Thus, in a series of 109 patients with leukemia and myelodysplastic …

Multiple rare alleles contribute to low plasma levels of HDL cholesterol.

Heritable variation in complex traits is generally considered to be conferred by common DNA sequence polymorphisms. We tested whether rare DNA sequence variants collectively contribute to variation in plasma levels of high density lipoprotein cholesterol (HDL-C). We sequenced three candidate genes (ABCA1, APOA1, and LCAT) that cause Mendelian forms of low HDL-C levels in individuals from a population-based study. Nonsynonymous sequence variants were significantly more common (16% versus 2%) in individuals with low HDL-C (<fifth percentile) than in those with high HDL-C (>95th percentile). Similar findings were obtained in an independent population, and biochemical studies indicated that most sequence variants in the low HDL-C group were functionally important. Thus, rare alleles with major phenotypic effects contribute significantly to low plasma HDL-C levels in the general population.

An integrated epigenetic and genetic approach to common human disease

Epigenetic information is heritable during cell division but is not contained within the DNA sequence itself. Despite increasing evidence for and interest in the role of epigenetics in human disease, particularly in cancer, virtually no epigenetic information is routinely or systematically measured at the genome level. The current population-based approach to common disease relates common DNA sequence variants to either disease status or incremental quantitative traits contributing to disease. Although this purely genetic approach is powerful and general, there is currently no conceptual framework to integrate epigenetic information. In this article, we propose an approach to common human disease that incorporates epigenetic variation into genetic studies. Epigenetic variation might also help to explain the late onset and progressive nature of most common diseases, the quantitative nature of complex traits and the role of environment in disease development, which a purely sequence-based approach might not.