Genomic mismatch scanning: a new approach to genetic linkage mapping

Diff-seq: A high throughput sequencing-based mismatch detection assay for DNA variant enrichment and discovery

Much of the within species genetic variation is in the form of single nucleotide polymorphisms (SNPs), typically detected by whole genome sequencing (WGS) or microarray-based technologies. However, WGS produces mostly uninformative reads that perfectly match the reference, while microarrays require genome-specific reagents. We have developed Diff-seq, a sequencing-based mismatch detection assay for SNP discovery without the requirement for specialized nucleic-acid reagents. Diff-seq leverages the Surveyor endonuclease to cleave mismatched DNA molecules that are generated after cross-annealing of a complex pool of DNA fragments. Sequencing libraries enriched for Surveyor-cleaved molecules result in increased coverage at the variant sites. Diff-seq detected all mismatches present in an initial test substrate, with specific enrichment dependent on the identity and context of the variation. Application to viral sequences resulted in increased observation of variant alleles in a biologically relevant context. Diff-Seq has the potential to increase the sensitivity and efficiency of high-throughput sequencing in the detection of variation.

Markov processes for modeling and analyzing a new genetic mapping method

This paper describes a set of stochastic processes that is useful for modeling and analyzing a new genetic mapping method. Some of the processes are Markov chains, and some are best described as functions of Markov chains. The central issue is boundary-crossing probabilities, which correspond top-values for the existence of genes for particular traits. The methods elaborated by Aldous (1989) provide very accurate approximatep-values, as spot-checked against simulations.

Markov processes for modeling and analyzing a new genetic mapping method

This paper describes a set of stochastic processes that is useful for modeling and analyzing a new genetic mapping method. Some of the processes are Markov chains, and some are best described as functions of Markov chains. The central issue is boundary-crossing probabilities, which correspond to p-values for the existence of genes for particular traits. The methods elaborated by Aldous (1989) provide very accurate approximate p-values, as spot-checked against simulations.

Two flavors of bulk segregant analysis in yeast

Genetic mapping methods typically rely upon genotyping many individuals in a mapping population. In contrast, bulk segregant analysis looks for biases in genotype in phenotyped pools of segregants. For relatively strong and genetically simple traits, it can be a fast, inexpensive approach. Although it is technically possible to use many genotyping platforms, microarray-based methods are convenient for their genome-wide coverage, ease of use, and quantitative output. Also, precise knowledge of polymorphic sites is not required. I present two methods for bulk segregant analysis using microarrays, one based on hybridization differences between polymorphisms, and the other using an enzymatic method for enriching identical by descent segments of the genome. The first method requires specialized array platforms, while the second, genomic mismatch scanning (GMS), is compatible with any microarray. Although the methods presented are with yeast, most steps are equivalent for other organisms.

Discovering tumor suppressor genes through genome-wide copy number analysis

Classical tumor suppressor gene discovery has largely involved linkage analysis and loss-of-heterozygosity (LOH) screens, followed by detailed mapping of relatively large chromosomal regions. Subsequent efforts made use of genome-wide PCR-based methods to detect rare homozygous deletions. More recently, high-resolution genomic arrays have been applied to cancer gene discovery. However, accurate characterization of regions of genomic loss is particularly challenging due to sample heterogeneity, the small size of deleted regions and the high frequency of germline copy number polymorphisms. Here, we review the application of genome-wide copy number analysis to the specific problem of identifying tumor suppressor genes.

Systematic identification of balanced transposition polymorphisms in Saccharomyces cerevisiae

High-throughput techniques for detecting DNA polymorphisms generally do not identify changes in which the genomic position of a sequence, but not its copy number, varies among individuals. To explore such balanced structural polymorphisms, we used array-based Comparative Genomic Hybridization (aCGH) to conduct a genome-wide screen for single-copy genomic segments that occupy different genomic positions in the standard laboratory strain of Saccharomyces cerevisiae (S90) and a polymorphic wild isolate (Y101) through analysis of six tetrads from a cross of these two strains. Paired-end high-throughput sequencing of Y101 validated four of the predicted rearrangements. The transposed segments contained one to four annotated genes each, yet crosses between S90 and Y101 yielded mostly viable tetrads. The longest segment comprised 13.5 kb near the telomere of chromosome XV in the S288C reference strain and Southern blotting confirmed its predicted location on chromosome IX in Y101. Interestingly, inter-locus crossover events between copies of this segment occurred at a detectable rate. The presence of low-copy repetitive sequences at the junctions of this segment suggests that it may have arisen through ectopic recombination. Our methodology and findings provide a starting point for exploring the origins, phenotypic consequences, and evolutionary fate of this largely unexplored form of genomic polymorphism.

Balanced structural polymorphisms are differences in the relative arrangement of genomic features within species that do not affect DNA copy number. Little is known about their prevalence or importance because they are difficult to observe. Here, we present a novel methodology for systematically identifying such polymorphisms based on the idea that single-copy DNA that occupies different genomic locations in two parents will segregate independently during meiosis and will therefore reveal itself as a copy number difference among a fraction of progeny. Comparative hybridization reveals multiple balanced structural polymorphisms that involve changes to gene order in two strains of yeast; the results are independently validated using paired-end whole genome shotgun sequencing. The longest transposed segment we identify comprises 13.5 kb near the telomere of chromosome XV in the S288C reference strain and contains several annotated genes. We map the location of this polymorphism in the non-reference strain using genome-wide genotypic data, which also reveals an appreciable frequency of ectopic recombination among transposed segment pairs. The breakpoints of the remaining polymorphisms are localized by the paired-end sequence data. Our work provides proof-of-principle for a very general approach to systematically identify all balanced genomic polymorphisms in two different genotypes and is a starting point for understanding the frequency, evolutionary origins, and functional consequences of this seldom-studied class of genomic structural variation in eukaryotes.

Robust physical methods that enrich genomic regions identical by descent for linkage studies: confirmation of a locus for osteogenesis imperfecta

BACKGROUND

The monogenic disease osteogenesis imperfecta (OI) is due to single mutations in either of the collagen genes ColA1 or ColA2, but within the same family a given mutation is accompanied by a wide range of disease severity. Although this phenotypic variability implies the existence of modifier gene variants, genome wide scanning of DNA from OI patients has not been reported. Promising genome wide marker-independent physical methods for identifying disease-related loci have lacked robustness for widespread applicability. Therefore we sought to improve these methods and demonstrate their performance to identify known and novel loci relevant to OI.

RESULTS

We have improved methods for enriching regions of identity-by-descent (IBD) shared between related, afflicted individuals. The extent of enrichment exceeds 10- to 50-fold for some loci. The efficiency of the new process is shown by confirmation of the identification of the Col1A2 locus in osteogenesis imperfecta patients from Amish families. Moreover the analysis revealed additional candidate linkage loci that may harbour modifier genes for OI; a locus on chromosome 1q includes COX-2, a gene implicated in osteogenesis.

CONCLUSION

Technology for physical enrichment of IBD loci is now robust and applicable for finding genes for monogenic diseases and genes for complex diseases. The data support the further investigation of genetic loci other than collagen gene loci to identify genes affecting the clinical expression of osteogenesis imperfecta. The discrimination of IBD mapping will be enhanced when the IBD enrichment procedure is coupled with deep resequencing.

Overview of nucleic acid arrays

Nucleic acid array technology refers to the use and fabrication of arrays containing thousands of nucleic acid samples bound to solid substrates such as glass microscope slides or silicon wafers. Because the physical area occupied by each sample is usually 50 to 200 mum in diameter, it is possible to assay nucleic acid samples representing entire genomes, ranging in size from 3,000 to 32,000 genes, on a single slide. Microarrays are good for, among other things, analyzing gene expression patterns, genotyping and genetic mapping, comparative genomic hybridization, polysome analysis, and DNA-protein interactions. This overview describes the technology and the uses, and provides valuable web site listings for readers to obtain additional information.

Shared genomic segment analysis. Mapping disease predisposition genes in extended pedigrees using SNP genotype assays

We examine the utility of high density genotype assays for predisposition gene localization using extended pedigrees. Results for the distribution of the number and length of genomic segments shared identical by descent among relatives previously derived in the context of genomic mismatch scanning are reviewed in the context of dense single nucleotide polymorphism maps. We use long runs of loci at which cases share a common allele identically by state to localize hypothesized predisposition genes. The distribution of such runs under the hypothesis of no genetic effect is evaluated by simulation. Methods are illustrated by analysis of an extended prostate cancer pedigree previously reported to show significant linkage to chromosome 1p23. Our analysis establishes that runs of simple single locus statistics can be powerful, tractable and robust for finding DNA shared between relatives, and that extended pedigrees offer powerful designs for gene detection based on these statistics.

Trinucleotide repeat instability: genetic features and molecular mechanisms

Trinucleotide repeat expansions are an important cause of inherited neurodegenerative disease. The expanded repeats are unstable, changing in size when transmitted from parents to offspring (intergenerational instability, "meiotic instability") and often showing size variation within the tissues of an affected individual (somatic mosaicism, "mitotic instability"). Repeat instability is a clinically important phenomenon, as increasing repeat lengths correlate with an earlier age of onset and a more severe disease phenotype. The tendency of expanded trinucleotide repeats to increase in length during their transmission from parent to offspring in these diseases provides a molecular explanation for anticipation (increasing disease severity in successive affected generations). In this review, I explore the genetic and molecular basis of trinucleotide repeat instability. Studies of patients and families with trinucleotide repeat disorders have revealed a number of factors that determine the rate and magnitude of trinucleotide repeat change. Analysis of trinucleotide repeat instability in bacteria, yeast, and mice has yielded additional insights. Despite these advances, the pathways and mechanisms underlying trinucleotide repeat instability in humans remain largely unknown. There are many reasons to suspect that this uniquely human phenomenon will significantly impact upon our understanding of development, differentiation and neurobiology.

Phenotypic and genetic analysis of a large family with migraine-associated vertigo

OBJECTIVES

To describe a large multigenerational family with migraine-associated vertigo (MAV) combining a detailed phenotypic and genetic analysis.

BACKGROUND

Migraine-associated vertigo is said to be highly prevalent in the general population and, like other migraine syndromes, its etiology is felt to have a strong genetic component. However, so far, there have been no reports of large families with MAV.

METHODS

Detailed clinical study was conducted on a large multigenerational family with MAV. Genetic study using identical-by-descent analysis with dense single nucleotide polymorphism (SNP) arrays was performed to examine consistent inheritance pattern among the affecteds.

RESULTS

Clinical features of MAV were variable although most had other migraine symptoms with at least some of their attacks. We did not find a region of the genome shared by all eight subjects with MAV indicating a polygenetic inheritance for MAV even in this single large family.

CONCLUSIONS

A region on 11q shared by most affected females may contain a susceptibility allele for MAV that is expressed exclusively or predominantly by women.

Episodic vertical oscillopsia with progressive gait ataxia: clinical description of a new episodic syndrome and evidence of linkage to chromosome 13q

We describe four families with late onset episodic vertical oscillopsia and progressive gait ataxia. Probands presented between the ages of 40 and 64 years with initial symptoms of episodic vertical oscillopsia and interictal downbeat nystagmus. A mild gait ataxia developed over several years. Triggers included physical exertion, alcohol and caffeine. Patients did not respond to acetazolamide. Genetic screening for episodic ataxia types 1 and 2, and spinocerebellar ataxias 1, 2, 3 and 6 were negative. Using ancestral identity by descent analysis and dense single nucleotide polymorphism (SNP) genotyping throughout the genome, an interval of 28.6 cM (approximately 14.2 Mb) on chromosome 13q12.11-q13.3, composed of 1259 SNPs, was shared between affected individuals in two of the four families and highlighted a region of suggestive linkage (LOD >2.7).

Identification of coding single nucleotide polymorphisms and mutations by combination of genome tiling arrays and enrichment/depletion of mismatch cDNAs

Genome tiling array technology combined with a method for both enrichment and depletion of mismatch-containing cDNA fragments offers a useful approach for detecting coding single nucleotide polymorphisms (cSNPs) and mutations in pooled cDNA samples. Enriched mismatch and perfect match cDNA samples from human primary melanoma cells and normal melanocytes were obtained by selection using mismatch repair thymine DNA glycosylase-bound beads. These cDNA samples were then labeled and hybridized to Encyclopedia of DNA Elements genome tiling arrays. The results revealed that the hybridization intensity values of potential cDNA variation regions of the enriched mismatch samples increased, whereas the hybridization intensity values of corresponding regions of the enriched perfect match samples decreased. Six potential mutations were confirmed by polymerase chain reaction product sequencing, including two novel heterozygous mutations in melanoma cells. We suggest that this strategy should increase the efficiency of both cSNP and mutation detection throughout the entire human genome and decrease the cost and complexity of genomewide analysis of cDNA variations.

Two-dimensional strandness-dependent electrophoresis: A method to characterize single-stranded DNA, double-stranded DNA, and RNA–DNA hybrids in complex samples

We describe two-dimensional strandness-dependent electrophoresis (2D-SDE) for quantification and length distribution analysis of single-stranded (ss) DNA fragments, double-stranded (ds) DNA fragments, RNA-DNA hybrids, and nicked DNA fragments in complex samples. In the first dimension nucleic acid molecules are separated based on strandness and length in the presence of 7 M urea. After the first-dimension electrophoresis all nucleic acid fragments are heat denatured in the gel. During the second-dimension electrophoresis all nucleic acid fragments are single-stranded and migrate according to length. 2D-SDE takes about 90 min and requires only basic skills and equipment. We show that 2D-SDE has many applications in analyzing complex nucleic acid samples including (1) estimation of renaturation efficiency and kinetics, (2) monitoring cDNA synthesis, (3) detection of nicked DNA fragments, and (4) estimation of quality and in vitro damage of nucleic acid samples. Results from 2D-SDE should be useful to validate techniques such as complex polymerase chain reaction, subtractive hybridization, cDNA synthesis, cDNA normalization, and microarray analysis. 2D-SDE could also be used, e.g., to characterize biological nucleic acid samples. Information obtained with 2D-SDE cannot be readily obtained with other methods. 2D-SDE can be used for preparative isolation of ssDNA fragments, dsDNA fragments, and RNA-DNA hybrids.

DNA reassociation using oscillating phenol emulsions

Reassociating double-stranded DNA from single-stranded components is necessary for many molecular genetics experiments. The choice of a DNA reassociation method is dictated by the complexity of the starting material. Reassociation of simple oligomers needs only slow cooling in an aqueous environment, whereas reannealing the many single-stranded DNAs of complex genomic mixtures requires both a phenol emulsion to accelerate DNA reassociation and dedicated equipment to maintain the emulsion. We present a method that is equally suitable for reassociating either simple or complex DNA mixtures. The Oscillating Phenol Emulsion Reassociation Technique (OsPERT) was primarily developed to prepare heteroduplex DNA from alkali-denatured high molecular weight human genomic DNA samples in which hundreds of thousands of fragments need to be reannealed, but the simplicity of the technique makes it practical for less demanding DNA reassociation applications.

Haplotypes in the gene encoding protein kinase c-beta (PRKCB1) on chromosome 16 are associated with autism

Autism is a developmental disorder characterized by impairments in social interaction and communication associated with repetitive patterns of interest or behavior. Autism is highly influenced by genetic factors. Genome-wide linkage and candidate gene association approaches have been used to try and identify autism genes. A few loci have repeatedly been reported linked to autism. Several groups reported evidence for linkage to a region on chromosome 16p. We have applied a direct physical identity-by-descent (IBD) mapping approach to perform a high-density (0.85 megabases) genome-wide linkage scan in 116 families from the AGRE collection. Our results confirm linkage to a region on chromosome 16p with autism. High-resolution single-nucleotide polymorphism (SNP) genotyping and analysis of this region show that haplotypes in the protein kinase c-beta gene are strongly associated with autism. An independent replication of the association in a second set of 167 trio families with autism confirmed our initial findings. Overall, our data provide evidence that the PRKCB1 gene on chromosome 16p may be involved in the etiology of autism.

Complex trait mapping in isolated populations: Are specific statistical methods required?

In this paper, we review the statistical methods that can be used in isolated populations to map genes involved in complex diseases. Our intention is to highlight the fact that if the features of population isolates may help in the identification of susceptibility factors for complex traits, the choice and design of methods for statistical analysis in these populations deserve particular care. We show that methods designed for outbred samples are generally not appropriate for isolated populations and could lead to false conclusions.

The probability density of the total IBD length over a single autosome in unilineal relationships

Several authors have studied identity by descent (IBD) by way of a continuous recombination process along a chromosome. Despite its potential uses in, for example, gene mapping or delineation of biological relationships there has been no exact algebraic result given for the probability density function of the IBD proportion in any familial relationship. Other authors have derived algebraic approximations in the case of half-sibs by way of the Poisson clumping heuristic and used computational methods to compute the distribution function of the IBD sharing for unilineal relationships. Here we provide a general numerical method for finding the density of IBD sharing that could be applied to any unilineal relationship and more importantly we derive algebraically an expression for the density for a grandparent-grandchild relationship. Initially we assume that recombination events occur at random along a chromosome, then go on to show how the method could be extended to incorporate a form of genetic interference.

Two-dimensional conformation-dependent electrophoresis (2D-CDE) to separate DNA fragments containing unmatched bulge from complex DNA samples

DNA fragments containing mispaired and modified bases, bulges, lesions and specific sequences have altered conformation. Methods for separating complex samples of DNA fragments based on conformation but independent of length have many applications, including (i) separation of mismatched or unmatched DNA fragments from those perfectly matched; (ii) simultaneous, diagnostic, mismatch scanning of multiple fragments; (iii) isolation of damaged DNA fragments from undamaged fragments; and (iv) estimation of reannealing efficiency of complex DNA samples. We developed a two-dimensional conformation-dependent electrophoresis (2D-CDE) method for separating DNA fragments based on length and conformation in the first dimension and only on length in the second dimension. Differences in migration velocity due to conformation were minimized during second dimension electrophoresis by introducing an intercalator. To test the method, we constructed 298 bp DNA fragments containing cytosine bulges ranging from 1 to 5 nt. Bulge-containing DNA fragments had reduced migration velocity in the first dimension due to altered conformation. After 2D-CDE, bulge-containing DNA fragments had migrated in front of an arc comprising heterogeneous fragments with regular conformation. This simple and robust method could be used in both analytical and preparative applications involving complex DNA samples.

Direct IBD mapping: identical-by-descent mapping without genotyping

Direct identical-by-descent (IBD) mapping is a technique, that combines genomic mismatch scanning (GMS) and DNA microarray technology, for mapping regions shared IBD between two individuals without locus-by-locus genotyping or sequencing. The lack of reagents has limited its widespread application. In particular, two key reagents have been limiting, 1). mismatch repair proteins MutS, L and H, and 2). genomic microarrays for identifying the genomic locations of the GMS-selected IBD fragments. Here, we describe steps that optimized the procedure and resources that will facilitate the development of direct IBD mapping.

A role for the mismatch repair system during incipient speciation in Saccharomyces

The cause of reproductive isolation between biological species is a major issue in the field of biology. Most explanations of hybrid sterility require either genetic incompatibilities between nascent species or gross physical imbalances between their chromosomes, such as rearrangements or ploidy changes. An alternative possibility is that genomes become incompatible at a molecular level, dependent on interactions between primary DNA sequences. The mismatch repair system has previously been shown to contribute to sterility in a hybrid between established yeast species by preventing successful meiotic crossing-over leading to aneuploidy. This system could also promote or reinforce the formation of new species in a similar manner, by making diverging genomes incompatible in meiosis. To test this possibility we crossed yeast strains of the same species but from diverse historical or geographic sources. We show that these crosses are partially sterile and present evidence that the mismatch repair system is largely responsible for this sterility.

Statistical analysis of direct identity-by-descent mapping

Genetic mismatch scanning has been suggested as a method for using affected pairs of ostensibly unrelated but putatively distantly related affecteds in isolated populations to map disease genes. We model the regions of identity-by-descent of these affected pairs as a continuous time two state process with unknown parameters that depend on the (unknown) relationships, and we estimate the unknown parameters from the observed data. Simulated data involving pairs of first to fourth cousins show that the procedure thus obtained has properties similar, albeit slightly inferior, to the case where the relationships of the affected pairs, hence the parameters governing the processes, are known.

An approach for global scanning of single nucleotide variations

Efficient global scanning of single nucleotide variations in DNA sequences between related, complex DNA samples remains a challenge. In the present article we present an approach to this problem. We have used immobilized thymidine DNA glycosylases to capture and enrich DNA fragments containing internal mismatched base pairs and separate these fragments as a pool from perfectly base-paired fragments as another pool. Enrichments of up to several hundredfold were obtained with one cycle of treatment, and all of the four groups of single nucleotide mismatches were fully covered by combining use of two thymine DNA glycosylases generated here. We have used a heterohybrid-orientating strategy for selective amplification of duplexes with one strand derived from each of two input DNA samples, which can also be used for selective amplification of duplexes with both strands derived from one of two input samples when desired. By combining these methods, the single nucleotide variations either between two DNA pools or within one DNA pool can be obtained in one process. This approach has been applied to the total cDNA from a human cell line and has several potential applications in mapping genetic variations, particularly global scanning of cDNA single nucleotide variations or polymorphisms, and finally high-throughput mapping of complex genetic traits.

Overview of nucleic acid arrays

Nucleic acid array technology refers to the use and fabrication of arrays containing thousands of nucleic acid samples bound to solid substrates such as glass microscope slides or silicon wafers. Because the physical area occupied by each sample is usually 50 to 200 micrometers in diameter, it is possible to assay nucleic acid samples representing entire genomes, ranging in size from 3,000 to 32,000 genes, on a single slide. Microarrays are useful for analyzing gene expression patterns, genotyping and genetic mapping, comparative genomic hybridization, polysome analysis, and DNA-protein interactions. This overview describes the technology and applications, and provides valuable web site listings for obtaining additional information.

On relationship inference using gamete identity by descent data

Related individuals are identical by descent (IBD) at a genetic locus if they share the same DNA material from a common ancestor. Continuous gamete IBD data consist of the lengths of (in order) IBD and non-IBD regions along the genomes for gametes segregating from two related individuals and can be used to distinguish different relationships. Under the assumption that the crossovers follow a Poisson process, we show that the exact calculation of the likelihood of a particular relationship for a given gamete IBD datum is tractable. Greatgrandparent--greatgrandchild and cousin relationships are used as examples to illustrate our methods.

PCR candidate region mismatch scanning: adaptation to quantitative, high-throughput genotyping

Linkage and association analyses were performed to identify loci affecting disease susceptibility by scoring previously characterized sequence variations such as microsatellites and single nucleotide polymorphisms. Lack of markers in regions of interest, as well as difficulty in adapting various methods to high-throughput settings, often limits the effectiveness of the analyses. We have adapted the Escherichia coli mismatch detection system, employing the factors MutS, MutL and MutH, for use in PCR-based, automated, high-throughput genotyping and mutation detection of genomic DNA. Optimal sensitivity and signal-to-noise ratios were obtained in a straightforward fashion because the detection reaction proved to be principally dependent upon monovalent cation concentration and MutL concentration. Quantitative relationships of the optimal values of these parameters with length of the DNA test fragment were demonstrated, in support of the translocation model for the mechanism of action of these enzymes, rather than the molecular switch model. Thus, rapid, sequence-independent optimization was possible for each new genomic target region. Other factors potentially limiting the flexibility of mismatch scanning, such as positioning of dam recognition sites within the target fragment, have also been investigated. We developed several strategies, which can be easily adapted to automation, for limiting the analysis to intersample heteroduplexes. Thus, the principal barriers to the use of this methodology, which we have designated PCR candidate region mismatch scanning, in cost-effective, high-throughput settings have been removed.

Distribution of genome shared identical by descent by two individuals in grandparent-type relationship

A methodology is introduced for numerical evaluation, with any given accuracy, of the cumulative probabilities of the proportion of genome shared identical by descent (IBD) on chromosome segments by two individuals in a grandparent-type relationship. Programs are provided in the popular software package Maple for rapidly implementing such evaluations in the cases of grandchild-grandparent and great-grandchild-great-grandparent relationships. Our results can be used to identify chromosomal segments that may contain disease genes. Also, exact P values in significance testing for resemblance of either a grandparent with a grandchild or a great-grandparent with a great-grandchild can be calculated. The genomic continuum model, with Haldane's model for the crossover process, is assumed. This is the model that has been used recently in the genetics literature devoted to IBD calculations. Our methodology is based on viewing the model as a special exponential family and elaborating on recent research results for such families.

A multivariate approach to affected-sib-pair analysis using highly dense molecular maps

A multivariate approach to affected-sib-pair analyses was performed to localize disease-susceptibility genes with a minimum number of type I errors (false positives). Using 1,155 independent affected sib pairs extracted from Problem 2A of the GAW10 data set, we were able to localize major genes (MG) 1 and 2. Using 30% of the affected-sib-pair sample (N = 337) we were able to localize MG1. False positives were not detected in either of these samples.

CIS--cloning of identical sequences between two complex genomes

Development of the methods permitting cloning of identical sequences between two sources of DNA can be very useful for many purposes, including isolation of disease genes. Here we describe a new method called CIS (cloning of identical sequences). A combination of digestion with MvnI, treatment with mung bean nuclease, UDG (uracil-DNA glycosylase) and PCR with 5'-methyl-dCTP and dUTP was used to isolate identical sequences between two micro-cell hybrid lines (MCH). In a control experiment, mouse MCH903.1 and MCH939.2 containing human chromosome 3 from different individuals, were compared using the CIS procedure. Only background fluorescence in-situ hybridization (FISH) was achieved. In another experiment, mouse MCH903.1, containing complete human chromosome 3, and rat MCH429.11, containing a part of human 3q from the same chromosome were compared. The experiment showed that the original MCH429.11 and the DNA purified using the CIS procedure had identical FISH patterns to human metaphase chromosomes, thus demonstrating the efficiency of CIS.

A resource of mapped human bacterial artificial chromosome clones

To date, despite the increasing number of genomic tools, there is no repository of ordered human BAC clones that covers entire chromosomes. This project presents a resource of mapped large DNA fragments that span eight human chromosomes at approximately 1-Mb resolution. These DNA fragments are bacterial artificial chromosome (BAC) clones anchored to sequence tagged site (STS) markers. This clone collection, which currently contains 759 mapped clones, is useful in a wide range of applications from microarray-based gene mapping to identification of chromosomal mutations. In addition to the clones themselves, we describe a database, GenMapDB (http://genomics.med.upenn.edu/genmapdb), that contains information about each clone in our collection.

A maize map standard with sequenced core markers, grass genome reference points and 932 expressed sequence tagged sites (ESTs) in a 1736-locus map

We have constructed a 1736-locus maize genome map containing1156 loci probed by cDNAs, 545 probed by random genomic clones, 16 by simple sequence repeats (SSRs), 14 by isozymes, and 5 by anonymous clones. Sequence information is available for 56% of the loci with 66% of the sequenced loci assigned functions. A total of 596 new ESTs were mapped from a B73 library of 5-wk-old shoots. The map contains 237 loci probed by barley, oat, wheat, rice, or tripsacum clones, which serve as grass genome reference points in comparisons between maize and other grass maps. Ninety core markers selected for low copy number, high polymorphism, and even spacing along the chromosome delineate the 100 bins on the map. The average bin size is 17 cM. Use of bin assignments enables comparison among different maize mapping populations and experiments including those involving cytogenetic stocks, mutants, or quantitative trait loci. Integration of nonmaize markers in the map extends the resources available for gene discovery beyond the boundaries of maize mapping information into the expanse of map, sequence, and phenotype information from other grass species. This map provides a foundation for numerous basic and applied investigations including studies of gene organization, gene and genome evolution, targeted cloning, and dissection of complex traits.

Enzymatic methods for mutation scanning

Enzymatic methods for mutation scanning still lack the sensitivity and specificity of the chemical cleavage of mismatch method. However developments in our understanding of the mismatch recognition process should lead to improvements. Several promising candidates exist with potential for more specific and sensitive mutation detection.

Exploring the new world of the genome with DNA microarrays

Thousands of genes are being discovered for the first time by sequencing the genomes of model organisms, an exhilarating reminder that much of the natural world remains to be explored at the molecular level. DNA microarrays provide a natural vehicle for this exploration. The model organisms are the first for which comprehensive genome-wide surveys of gene expression patterns or function are possible. The results can be viewed as maps that reflect the order and logic of the genetic program, rather than the physical order of genes on chromosomes. Exploration of the genome using DNA microarrays and other genome-scale technologies should narrow the gap in our knowledge of gene function and molecular biology between the currently-favoured model organisms and other species.

Genomics and array technology

Genome projects are providing vast amounts of sequence data. This raw material makes possible a completely new era of experimental approaches. Among these, DNA array technology, which allows one to assay thousands of unique nucleic acid samples simultaneously, will be important in genomic research, and the results of this research are likely to affect virtually every field of biology. DNA array technology is still in its infancy, but many have demonstrated its power by using it for such diverse applications as global monitoring of gene expression, mutation detection, and genetic mapping.

The relative power of family-based and case-control designs for linkage disequilibrium studies of complex human diseases I. DNA pooling

We consider statistics for analyzing a variety of family-based and nonfamily-based designs for detecting linkage disequilibrium of a marker with a disease susceptibility locus. These designs include sibships with parents, sibships without parents, and use of unrelated controls. We also provide formulas for and evaluate the relative power of different study designs using these statistics. In this first paper in the series, we derive statistical tests based on data derived from DNA pooling experiments and describe their characteristics. Although designs based on affected and unaffected sibs without parents are usually robust to population stratification, they suffer a loss of power compared with designs using parents or unrelateds as controls. Although increasing the number of unaffected sibs improves power, the increase is generally not substantial. Designs including sibships with multiple affected sibs are typically the most powerful, with any of these control groups, when the disease allele frequency is low. When the allele frequency is high, however, designs with unaffected sibs as controls do not retain this advantage. In designs with parents, having an affected parent has little impact on the power, except for rare dominant alleles, where the power is increased compared with families with no affected parents. Finally, we also demonstrate that for sibships with parents, only the parents require individual genotyping to derive the TDT statistic, whereas all the offspring can be pooled. This can potentially lead to considerable savings in genotyping, especially for multiplex sibships. The formulas and tables we derive should provide some guidance to investigators designing nuclear family-based linkage disequilibrium studies for complex diseases.

The integration of microarray information in the drug development process

In the past year, microarray technologies have moved beyond the proof-of-principle stage. Microarrays are now being used for genome-wide expression monitoring, large-scale polymorphism screening and mapping, and for the evaluation of drug candidates.

Direct allelic variation scanning of the yeast genome

As more genomes are sequenced, the identification and characterization of the causes of heritable variation within a species will be increasingly important. It is demonstrated that allelic variation in any two isolates of a species can be scanned, mapped, and scored directly and efficiently without allele-specific polymerase chain reaction, without creating new strains or constructs, and without knowing the specific nature of the variation. A total of 3714 biallelic markers, spaced about every 3.5 kilobases, were identified by analyzing the patterns obtained when total genomic DNA from two different strains of yeast was hybridized to high-density oligonucleotide arrays. The markers were then used to simultaneously map a multidrug-resistance locus and four other loci with high resolution (11 to 64 kilobases).

Relationship information contained in gamete identity by descent data

We consider idealized gamete identity by descent (IBD) data which consists of the lengths of IBD and non-IBD regions along the genome for gametes segregating from two related individuals. Information on the relationship between the individuals is contained in the pattern of lengths, with the power of the likelihood ratio test to reject one relationship in favor of another giving a measure of the information contained in the data. We model crossovers with a Poisson process and, under this assumption, present a novel Monte Carlo method for calculating the likelihood of a particular relationship for a given data set. The method provides a way to calculate the information content of data and find the maximum power that tests of relationship can achieve. Simulated data from cousin and greatgrandparent-greatgrandchild relationships is analyzed as an example.

Scission of DNA at a preselected sequence using a single-strand-specific chemical nuclease

BACKGROUND

We were interested in developing a protocol for cleaving large DNAs specifically. Previous attempts to develop such methods have failed to work because of high levels of nonspecific background scission.

RESULTS

R-loop formation was chosen for sequence-specific targeting, a method of hybridization whereby an RNA displaces a DNA strand of identical sequence in 70% formamide using Watson-Crick base-pairing, leading to a three-stranded structure. R-loops are stabilized in aqueous solution by modifying the bases with chemical reagents. The R-loop was cleaved using a novel nuclease prepared from the Thr48-->Cys mutant of the single-strand-specific M-13 gene V protein (GVP), which was alkylated with 5-(iodoacetamido-beta-alanyl)1,10-phenanthroline. The cleavage products of the pGEM plasmid were cloned in to the pCR 2.1-TOPO vector. Adenovirus 2 DNA (35.8 kb; tenfold larger than the pGEM plasmid) was also cleaved quantitatively at a preselected sequence.

CONCLUSIONS

A new method for cleaving duplex DNA at any preselected sequence was developed. The cleavage method relies on the chemical conversion of M-13 GVP into a nuclease, reflecting GVP's specificity for single-stranded DNA. The GVP chimera is the first example of a semisynthetic secondary structure specific nuclease. The chemical nuclease activity of 1,10-phenanthroline-copper is uniquely suited to this technique because it oxidizes the deoxyribose moiety without generating diffusible intermediates, providing clonable DNA fragments. The protocol could be useful in generating large DNA fragments for mapping the contiguity of probes or defining the exon-intron structure of transcription units.

Linkage-disequilibrium mapping without genotyping

Genomic mismatch scanning (GMS) is a technique that enriches for regions of identity by descent (IBD) between two individuals without the need for genotyping or sequencing. Regions of IBD selected by GMS are mapped by hybridization to a microarray containing ordered clones of genomic DNA from chromosomes of interest. Here we demonstrate the feasibility and efficacy of this form of linkage-mapping, using congenital hyperinsulinism (HI), an autosomal recessive disease, whose relatively high frequency in Ashkenazi Jews suggests a founder effect. The gene responsible (SUR1) encodes the sulfonylurea receptor, which maps to chromosome 11p15.1. We show that the combination of GMS and hybridization of IBD products to a chromosome-11 microarray correctly maps the HI gene to a 2-Mb region, thereby demonstrating linkage-disequilibrium mapping without genotyping.

Cluster analysis of the genetic heterogeneity and disease distributions in purebred dog populations

Purebred dog populations have been subject to strong selection which has resulted in extreme differences between breeds and decreased heterogeneity within breeds. As a result, breed-specific inherited diseases have accumulated in many populations. The aim of this study was to analyse genetic heterogeneity in relation to the distribution of elbow dysplasia in labrador retrievers, portosystemic shunts in Irish wolfhounds, and hepatic copper toxicosis, in Bedlington terriers. Decreased heterogeneity was demonstrated in the multiple genetic interrelations in the three populations. In pedigrees containing seven generations of ancestors, the average number of common ancestors in all pair-wise combinations of dogs was five to six (range 0 to 18). These complex interrelationships were resolved by a cluster analysis on matrices of relatedness. This analysis gave clusters of highly related animals, the average relatedness of these clusters, and the average relatedness of the entire population, as expressions of its genetic variability. The mean relatedness was 0.032 for Irish wolfhounds and Bedlington terriers, and 0.002 for labrador retrievers. The labrador retriever cohort was resolved into 31 clusters, and all cases of elbow dysplasia were concentrated in five highly related clusters with an overall incidence of 17 per cent. The Bedlington terrier cohort consisted of 12 clusters which all contained cases of copper toxicosis, with an overall incidence of 46 per cent. The Irish wolfhounds were divided into 14 clusters with a disease incidence of 4 per cent. Dogs with portosystemic shunts were found in four averagely related clusters. A genetic distribution became obvious only when relatedness due to common ancestors of the cases was used as a criterion, and the cases were then concentrated in five highly related clusters.

Genomic mismatch scanning identifies human genomic DNA shared identical by descent

Genomic mismatch scanning (GMS) is a high-throughput, high-resolution identity by descent mapping technique that enriches for genomic DNA fragments that are shared between related individuals. In GMS, DNA heteroduplexes are formed from restriction-digested genomic DNA fragments from two relatives. Mismatch-free DNA heteroduplexes, likely representing DNA shared identical by descent between the two individuals, are relatively purified by depleting the mismatch-containing heteroduplexes using the Escherichia coli mismatch repair proteins and exonuclease. Here, we demonstrate using quantitative microsatellite genotyping that, despite the complexity of the human genome, GMS can enrich the majority of restriction fragments that are identical by descent between two related humans. As the entire genome is selected in GMS, an extraordinarily dense set of markers (up to 200,000 markers) may be screened in parallel. The demonstration of the molecular enrichment of identical DNA fragments in the context of the whole human genome establishes conditions for the application of GMS to human genetics. This forms a frame-work for the further development of GMS as a hybridization-based mapping technique that utilizes DNA microarray technology to map the selected identical by descent DNA fragments.

Enrichment for loci identical-by-descent between pairs of mouse or human genomes by genomic mismatch scanning

Mapping genes that underlie complex genetic traits, including genes that determine susceptibility to common diseases, requires an efficient method for high-resolution genotyping. Single-nucleotide differences between pairs of allelic sequences from unrelated individuals occur approximately once in every kilobase. Genomic mismatch scanning (GMS), by analyzing numerous single-nucleotide polymorphisms in a single genome-wide step, offers a potentially powerful and efficient approach to linkage analysis. GMS, originally developed in a yeast system, is shown here to be applicable to the more complex mouse and human genomes.

Yeast microarrays for genome wide parallel genetic and gene expression analysis

We have developed high-density DNA microarrays of yeast ORFs. These microarrays can monitor hybridization to ORFs for applications such as quantitative differential gene expression analysis and screening for sequence polymorphisms. Automated scripts retrieved sequence information from public databases to locate predicted ORFs and select appropriate primers for amplification. The primers were used to amplify yeast ORFs in 96-well plates, and the resulting products were arrayed using an automated micro arraying device. Arrays containing up to 2,479 yeast ORFs were printed on a single slide. The hybridization of fluorescently labeled samples to the array were detected and quantitated with a laser confocal scanning microscope. Applications of the microarrays are shown for genetic and gene expression analysis at the whole genome level.