The present invention is a method and compositions for primer extension target enrichment of nucleic acids and improvements thereto including simultaneously enriching for RNA and DNA and optionally sequencing the enriched products. An embodiment of the present invention includes a method comprising the steps of: hybridizing a target-specific primer to a target DNA or RNA, wherein the primer comprises a target-binding region and a region of complementarity to an adaptor; extending the primer with a DNA polymerase or reverse transcriptase to form a primer extension product; contacting the product with an adaptor comprising a longer strand with a 5′-overhang having complementarity to said primer and a shorter strand comprising a universal priming site; hybridizing the adaptor to the product; and ligating one strand of the adaptor to the product to form a ligation product.

The present invention is a method and compositions for primer extension target enrichment of nucleic acids and improvements thereto including simultaneously enriching for RNA and DNA and optionally sequencing the enriched products. An embodiment of the present invention includes a method comprising the steps of: hybridizing a target-specific primer to a target DNA or RNA, wherein the primer comprises a target-binding region and a region of complementarity to an adaptor; extending the primer with a DNA polymerase or reverse transcriptase to form a primer extension product; contacting the product with an adaptor comprising a longer strand with a 5′-overhang having complementarity to said primer and a shorter strand comprising a universal priming site; hybridizing the adaptor to the product; and ligating one strand of the adaptor to the product to form a ligation product.

The present invention is a method and compositions for primer extension target enrichment of nucleic acids and improvements thereto including simultaneously enriching for RNA and DNA and optionally sequencing the enriched products. An embodiment of the present invention includes a method comprising the steps of: hybridizing a target-specific primer to a target DNA or RNA, wherein the primer comprises a target-binding region and a region of complementarity to an adaptor; extending the primer with a DNA polymerase or reverse transcriptase to form a primer extension product; contacting the product with an adaptor comprising a longer strand with a 5′-overhang having complementarity to said primer and a shorter strand comprising a universal priming site; hybridizing the adaptor to the product; and ligating one strand of the adaptor to the product to form a ligation product.

The invention provides methods for simultaneously amplifying multiple nucleic acid regions of interest in one reaction volume as well as methods for selecting a library of primers for use in such amplification methods. The invention also provides library of primers with desirable characteristics, such as minimal formation of amplified primer dimers or other non-target amplicons.

The invention provides methods for simultaneously amplifying multiple nucleic acid regions of interest in one reaction volume as well as methods for selecting a library of primers for use in such amplification methods. The invention also provides library of primers with desirable characteristics, such as minimal formation of amplified primer dimers or other non-target amplicons.

Disclosed herein include methods and compositions for selectively amplifying and/or extending nucleic acid target molecules in a sample. The methods and compositions can, for example, reduce the amplification and/or extension of undesirable nucleic acid species in the sample, and/or allow selective removal of undesirable nucleic acid species in the sample.

Disclosed herein include methods and compositions for selectively amplifying and/or extending nucleic acid target molecules in a sample. The methods and compositions can, for example, reduce the amplification and/or extension of undesirable nucleic acid species in the sample, and/or allow selective removal of undesirable nucleic acid species in the sample.

The present invention relates to a method of whole genome sequencing of a single cell or cell-group for identification of single nucleotide variants, determining chromosome structural variations, or determining phasing information in the genome of the single cell or cell-group. Methods of preparing an indexed DNA library for sequencing of nucleic acid molecules; preparing an indexed DNA library for whole genome sequencing of single cells or cell-groups for the identification of single nucleotide variants, determining chromosome structural variations, or determining phasing information in the genome of the single cells or cell-groups; and whole genome sequencing of a single cell or cell-group to provide data for the identification of single nucleotide variants (SNVs), determining chromosome structural variations, or determining phasing information in the genome of the single cell or cell-group are also described.

The present invention relates to a method of whole genome sequencing of a single cell or cell-group for identification of single nucleotide variants, determining chromosome structural variations, or determining phasing information in the genome of the single cell or cell-group. Methods of preparing an indexed DNA library for sequencing of nucleic acid molecules; preparing an indexed DNA library for whole genome sequencing of single cells or cell-groups for the identification of single nucleotide variants, determining chromosome structural variations, or determining phasing information in the genome of the single cells or cell-groups; and whole genome sequencing of a single cell or cell-group to provide data for the identification of single nucleotide variants (SNVs), determining chromosome structural variations, or determining phasing information in the genome of the single cell or cell-group are also described.

The present invention relates to a method for the highly specific, targeted capture of regions of human genomes and transcriptomes from the blood, i.e. from cell free circulating DNA, exosomes, microRNA, circulating tumor cells, or total blood cells, to allow for the highly sensitive detection of mutation, expression, copy number, translocation, alternative splicing, and methylation changes using combined nuclease, ligation, polymerase, and massively parallel sequencing reactions. The method generates a collection of different circular chimeric single-stranded nucleic acid constructs, suitable for sequencing on multiple platforms. In some embodiments, each construct of the collection comprised a first single stranded segment of original genomic DNA from a host organism and a second single stranded synthetic nucleic acid segment that is linked to the first single stranded segment and comprises a nucleotide sequence that is exogenous to the host organism. These chimeric constructs are suitable for identifying and enumerating mutations, copy changes, translocations, and methylation changes. In other embodiments, input mRNA, lncRNA, or miRNA is used to generate circular DNA products that reflect the presence and copy number of specific mRNA's, lncRNA's splice-site variants, translocations, and miRNA.