The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing.

Methods, devices and systems for analyzing precious samples of cells, including single cells are provided. The methods, devices, and systems in various embodiments of the invention are used to assess genomic heterogeneity, which has been recognized as a central feature of many cancers and plays a critical role in disease initiation, progression, and response to treatment. The methods devices and systems are also used to analyze embryonic biopsies for preimplantation genetic diagnosis (PGD). In one embodiment, the devices, systems and methods provided herein allow for the construction of genomic and RNA-seq libraries without a pre-amplification step.

Methods, devices and systems for analyzing precious samples of cells, including single cells are provided. The methods, devices, and systems in various embodiments of the invention are used to assess genomic heterogeneity, which has been recognized as a central feature of many cancers and plays a critical role in disease initiation, progression, and response to treatment. The methods devices and systems are also used to analyze embryonic biopsies for preimplantation genetic diagnosis (PGD). In one embodiment, the devices, systems and methods provided herein allow for the construction of genomic and RNA-seq libraries without a pre-amplification step.

The disclosure provides novel methods and compositions for gene editing. In particular, the disclosure relates to compositions and methods of making nucleic acid donor templates for highly efficient and precise gene editing.

The disclosure provides novel methods and compositions for gene editing. In particular, the disclosure relates to compositions and methods of making nucleic acid donor templates for highly efficient and precise gene editing.

The present disclosure provides a method of treating a cancer in a patient who has undergone a first anti-cancer therapy. Also provided is a method for monitoring treatment response and minimum residual disease in a neoadjuvantly treated cancer patient. Methods for primer design are also disclosed. The present disclosure provides several tools for increasing the sensitivity and analytical precision of the disclosed methods for monitoring ctDNA.

The present disclosure provides a method of treating a cancer in a patient who has undergone a first anti-cancer therapy. Also provided is a method for monitoring treatment response and minimum residual disease in a neoadjuvantly treated cancer patient. Methods for primer design are also disclosed. The present disclosure provides several tools for increasing the sensitivity and analytical precision of the disclosed methods for monitoring ctDNA.

The present invention relates to a method for a non-specific amplification of a natural short-fragment nucleic acid, comprising the following steps: (1) performing end repair on the natural short-fragment nucleic acid to obtain an end-repaired nucleic acid; (2) connecting the end-repaired nucleic acid to a double-stranded linker to obtain a ligation product, in which each strand of the double-stranded linker contains only three bases; (3) performing PCR amplification on the ligation product using a PCR primer labeled with deoxyuridine to obtain a PCR product, in which the PCR primer is completely or partially complementary to a strand of the double-stranded linker and contains only three bases; and (4) digesting the PCR product by using an enzyme having a deoxyuridine cleavage function, followed by digesting the PCR product by using an enzyme with both 5′.fwdarw.3′ polymerase activity and 3′.fwdarw.5′ exonuclease activity in the presence of a deoxynucleotide solution to obtain a non-specific amplification product of the natural short-fragment nucleic acid. The deoxynucleotide solution only contains the complementary base of the base lacking in the primer. The present invention also relates to a kit for implementing the aforementioned method.

The present invention relates to a method for a non-specific amplification of a natural short-fragment nucleic acid, comprising the following steps: (1) performing end repair on the natural short-fragment nucleic acid to obtain an end-repaired nucleic acid; (2) connecting the end-repaired nucleic acid to a double-stranded linker to obtain a ligation product, in which each strand of the double-stranded linker contains only three bases; (3) performing PCR amplification on the ligation product using a PCR primer labeled with deoxyuridine to obtain a PCR product, in which the PCR primer is completely or partially complementary to a strand of the double-stranded linker and contains only three bases; and (4) digesting the PCR product by using an enzyme having a deoxyuridine cleavage function, followed by digesting the PCR product by using an enzyme with both 5′.fwdarw.3′ polymerase activity and 3′.fwdarw.5′ exonuclease activity in the presence of a deoxynucleotide solution to obtain a non-specific amplification product of the natural short-fragment nucleic acid. The deoxynucleotide solution only contains the complementary base of the base lacking in the primer. The present invention also relates to a kit for implementing the aforementioned method.

The present disclosure relates to a method for constructing a whole genome high-throughput sequencing library comprising the following steps: (1) extracting a sample gDNA; (2) fragmenting said sample gDNA by enzyme cleavage, filling ends of the gDNA and adding A base to the gDNA fragments to obtain an A-added gDNA; (3) connecting the A-added gDNA with a linker combination to obtain a connected produce, said linker combination comprises two parts: a Y-shaped reverse linker and a high GC clamp linker; (4) purifying said connected product to obtain a purified product; and (5) screening the fragment of said purified product to obtain a sequencing library. The present disclosure also relates to a kit for constructing a whole genome high-throughput sequencing library.