Described herein is a method of sequencing a template that comprises a direct repeat, comprising: (a) in the same reaction, hybridizing a primer to a first site that is upstream of the first repeat sequence and hybridizing a primer to a second site that is upstream of the second repeat sequence, wherein the first and second sites are: (i) upstream of the first and second repeat sequences, respectively, and (ii) equidistant from the first and second repeat sequences; and (b) subjecting the hybridization product of (a) to a sequencing-by-synthesis sequencing reaction to produce a sequence read that comprises a combination of the first and second repeat sequences.

Provided herein are methods, compositions, and systems for processing nucleic acids from individual cells or cell populations. Cells are co-partitioned and processed, allowing for analysis of a variety of types of RNA from cells while minimizing ribosomal RNA species. The present invention enables high-throughput measurement of full length RNA from single cells with a streamlined workflow.

Provided herein are methods, compositions, and systems for processing nucleic acids from individual cells or cell populations. Cells are co-partitioned and processed, allowing for analysis of a variety of types of RNA from cells while minimizing ribosomal RNA species. The present invention enables high-throughput measurement of full length RNA from single cells with a streamlined workflow.

The methods and assays described herein relate to detection, diagnosis, and treatment of lung cancer, e.g., by detecting the level of expression of certain miRNAs described herein and/or by therapeutically increasing the level of those miRNAs.

The invention provides methods, systems, and computer readable medium for detecting ploidy of chromosome segments or entire chromosomes, for detecting single nucleotide variants and for detecting both ploidy of chromosome segments and single nucleotide variants. In some aspects, the invention provides methods, systems, and computer readable medium for detecting cancer or a chromosomal abnormality in a gestating fetus.

The invention provides methods, systems, and computer readable medium for detecting ploidy of chromosome segments or entire chromosomes, for detecting single nucleotide variants and for detecting both ploidy of chromosome segments and single nucleotide variants. In some aspects, the invention provides methods, systems, and computer readable medium for detecting cancer or a chromosomal abnormality in a gestating fetus.

Described herein is a method of sequencing a template that comprises a direct repeat, comprising: (a) in the same reaction, hybridizing a primer to a first site that is upstream of the first repeat sequence and hybridizing a primer to a second site that is upstream of the second repeat sequence, wherein the first and second sites are: (i) upstream of the first and second repeat sequences, respectively, and (ii) equidistant from the first and second repeat sequences; and (b) subjecting the hybridization product of (a) to a sequencing-by-synthesis sequencing reaction to produce a sequence read that comprises a combination of the first and second repeat sequences.

Described herein is a method of sequencing a template that comprises a direct repeat, comprising: (a) in the same reaction, hybridizing a primer to a first site that is upstream of the first repeat sequence and hybridizing a primer to a second site that is upstream of the second repeat sequence, wherein the first and second sites are: (i) upstream of the first and second repeat sequences, respectively, and (ii) equidistant from the first and second repeat sequences; and (b) subjecting the hybridization product of (a) to a sequencing-by-synthesis sequencing reaction to produce a sequence read that comprises a combination of the first and second repeat sequences.

The present invention relates a system and method for cancer-cell specific transcription identification. The method including: receiving nucleic acid data from one or more samples; determining variant allele fraction (VAF) of markers in ribonucleic acid (RNA) in the nucleic acid data and markers for deoxyribonucleic acid (DNA) in the nucleic acid data; comparing the VAF of the RNA relative to the DNA for each of the markers; and outputting the comparison as a quantification of cancer-cell specific changes in transcriptional output as a marker of prognosis or therapeutic response in cancer.

The present invention relates a system and method for cancer-cell specific transcription identification. The method including: receiving nucleic acid data from one or more samples; determining variant allele fraction (VAF) of markers in ribonucleic acid (RNA) in the nucleic acid data and markers for deoxyribonucleic acid (DNA) in the nucleic acid data; comparing the VAF of the RNA relative to the DNA for each of the markers; and outputting the comparison as a quantification of cancer-cell specific changes in transcriptional output as a marker of prognosis or therapeutic response in cancer.