Robert J. Lipshutz

High density synthetic oligonucleotide arrays

Experimental genomics involves taking advantage of sequence information to investigate and understand the workings of genes, cells and organisms. We have developed an approach in which sequence information is used directly to design high–density, two–dimensional arrays of synthetic oligonucleotides. The GeneChip® probe arrays are made using spatially patterned, light–directed combinatorial chemical synthesis, and contain up to hundreds of thousands of different oligonucleotides on a small glass surface. The arrays have been designed and used for quantitative and highly parallel measurements of gene expression, to discover polymorphic loci and to detect the presence of thousands of alternative alleles. Here, we describe the fabrication of the arrays, their design and some specific applications to high–throughput genetic and cellular analysis.

Characterization of single-nucleotide polymorphisms in coding regions of human genes

Nature Genet. 14, 415– 420 (1996). Due to a cloning error, the sequence reported for ING1 was incorrect. The error appears to have been a result of a compression introducing a frameshift and of the ING1 gene encoding several differentially spliced isoforms that contain a common 3′ exon, one of whichis of a size very similar to that reported in the publication above.

Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis

Sequence variation in human genes is largely confined to single-nucleotide polymorphisms (SNPs) and is valuable in tests of association with common diseases and pharmacogenetic traits. We performed a systematic and comprehensive survey of molecular variation to assess the nature, pattern and frequency of SNPs in 75 candidate human genes for blood-pressure homeostasis and hypertension. We assayed 28 Mb (190 kb in 148 alleles) of genomic sequence, comprising the 5´ and 3´ untranslated regions (UTRs), introns and coding sequence of these genes, for sequence differences in individuals of African and Northern European descent using high-density variant detection arrays (VDAs). We identified 874 candidate human SNPs, of which 22% were confirmed by DNA sequencing to reveal a discordancy rate of 21% for VDA detection. The SNPs detected have an average minor allele frequency of 11%, and 387 are within the coding sequence (cSNPs). Of all cSNPs, 54% lead to a predicted change in the protein sequence, implying a high level of human protein diversity. These protein-altering SNPs are 38% of the total number of such SNPs expected, are more likely to be population-specific and are rarer in the human population, directly demonstrating the effects of natural selection on human genes. Overall, the degree of nucleotide polymorphism across these human genes, and orthologous great ape sequences, is highly variable and is correlated with the effects of functional conservation on gene sequences.

Determination of ancestral alleles for human single-nucleotide polymorphisms using high-density oligonucleotide arrays.

Here we report the application of high-density oligonucleotide array (DNA chip)-based analysis to determine the distant history of single nucleotide polymorphisms (SNPs) in current human populations. We analysed orthologues for 397 human SNP sites (identified in CEPH pedigrees from Amish, Venezuelan and Utah populations) from 23 common chimpanzee, 19 pygmy chimpanzee and 11 gorilla genomic DNA samples. From this data we determined 214 proposed ancestral alleles (the sequence found in the last common ancestor of humans and chimpanzees). In a diverse human population set, we found that SNP alleles with higher frequencies were more likely to be ancestral than less frequently occurring alleles. There were, however, exceptions. We also found three shared human/pygmy chimpanzee polymorphisms, all involving CpG dinucleotides, and two shared human/gorilla polymorphisms, one involving a CpG dinucleotide. We demonstrate that microarray-based assays allow rapid comparative sequence analysis of intra- and interspecies genetic variation.

Genome-wide mapping with biallelic markers in Arabidopsis thaliana

Single-nucleotide polymorphisms, as well as small insertions and deletions (here referred to collectively as simple nucleotide polymorphisms, or SNPs), comprise the largest set of sequence variants in most organisms. Positional cloning based on SNPs may accelerate the identification of human disease traits and a range of biologically informative mutations. The recent application of high-density oligonucleotide arrays to allele identification has made it feasible to genotype thousands of biallelic SNPs in a single experiment. It has yet to be established, however, whether SNP detection using oligonucleotide arrays can be used to accelerate the mapping of traits in diploid genomes. The cruciferous weed Arabidopsis thaliana is an attractive model system for the construction and use of biallelic SNP maps. Although important biological processes ranging from fertilization and cell fate determination to disease resistance have been modelled in A. thaliana, identifying mutations in this organism has been impeded by the lack of a high-density genetic map consisting of easily genotyped DNA markers. We report here the construction of a biallelic genetic map in A. thaliana with a resolution of 3.5 cM and its use in mapping Eds16, a gene involved in the defence response to the fungal pathogen Erysiphe orontii. Mapping of this trait involved the high-throughput generation of meiotic maps of F2 individuals using high-density oligonucleotide probe array-based genotyping. We developed a software package called InterMap and used it to automatically delimit Eds16 to a 7-cM interval on chromosome 1. These results are the first demonstration of biallelic mapping in diploid genomes and establish means for generalizing SNP-based maps to virtually any genetic organism.

Towards DNA Sequencing Chips

DNA sequencing is an important technology for the determination of the sequences of nucleotides that make up a given DNA fragment. In view of the limitations of current sequencing technology, it would be advantageous to have a DNA sequencing method that provides the sequences of long DNA fragments and is amenable to automation. Sequencing by Hybridization (SBH) is a challenging alternative to the classical sequencing methods. The basic approach is to build an array (Sequencing Chip) of short DNA fragments of lenght l and to use biochemical methods for finding all substrings of lenght l of an unknown DNA fragment. Combinatorial algorithms are then used to reconstruct the sequence of the fragment from the l-tuple composition. In this article we review biochemical, mathematical, and technological aspects of SBH and present a new sequencing chip design which might allow significant chip miniaturization without loss of the resolution of the method.

Likelihood DNA Sequencing By Hybridization

Sequencing by hybridization (SBH) extracts local sequence information from a DNA fragment using hybridization with oligonucleotides and then reconstructs the sequence using the derived information. We describe an improvement to the SBH methodology which will allow it to work efficiently in the presence of hybridization errors. In particular, given a set of hybridizing probes, and the empirically derived rates of false positive and false negative hybridization, we can estimate the most likely DNA fragment to have produced the set of probes, and then estimate the probability that it generated the hybridization data. This methodology extends earlier results by identifying the most probable fragment to have generated the actual hybridization data. The methodology described will also generate longer unambiguous sequence fragments without the use of overlapping fragments.

Combinatorial Algorithms for Design of DNA Arrays

Optimal design of DNA arrays requires the development of algorithms with two-fold goals: reducing the effects caused by unintended illumination (border length minimization problem) and reducing the complexity of masks (mask decomposition problem). We describe algorithms that reduce the number of rectangles in mask decomposition by 20-30% as compared to a standard array design under the assumption that the arrangement of oligonucleotides on the array is fixed. This algorithm produces provably optimal solution for all studied real instances of array design. We also address the difficult problem of finding an arrangement which minimizes the border length and come up with a new idea of threading that significantly reduces the border length as compared to standard designs.

Advanced DNA sequencing technologies

Abstract Methods of DNA sequencing are advancing rapidly. Driven by large-scale sequencing projects, numerous improvements to the traditional sequencing methods of Sanger and Maxam-Gilbert have been developed and are becoming more widely used. In addition, entirely new sequencing and sequence analysis methods have been demonstrated and should soon become widely accessible.

POLYNUCLEOTIDE ARRAYS FOR GENETIC SEQUENCE ANALYSIS

We describe a new paradigm for genetic analysis based upon high density arrays of polynucleotide probes. Methods for light-directed polynucleotide array synthesis, as well as array packaging, sample preparation, array hybridization, epifluorescence confocal scanning, and data analysis are described. Applications to discovery, genotyping, expression, and resquencing are presented.