Abstract: Systems and methods are provided for quality control for biological testing. One embodiment is a system that includes a liquid handler that applies samples of genetic material to a test plate comprising an array of wells, a Polymerase Chain Reaction (PCR) device that amplifies the genetic material, and an analysis device that determines, based on a change in visual appearance of each well, a numerical value indicating whether a corresponding sample is representative of a disease state. The system also includes a quality assurance server that identifies a pattern of the numerical values, and determines a likelihood of the pattern. In an event that the likelihood is less than a threshold value, the quality assurance server flags the test plate as potentially contaminated, and in an event that the likelihood exceeds the threshold value, the quality assurance server refrains from flagging the test plate as potentially contaminated.

Abstract: Systems and methods are provided for quality control for biological testing. One embodiment is a system that includes a liquid handler that applies samples of genetic material to a test plate comprising an array of wells, a Polymerase Chain Reaction (PCR) device that amplifies the genetic material, and an analysis device that determines, based on a change in visual appearance of each well, a numerical value indicating whether a corresponding sample is representative of a disease state. The system also includes a quality assurance server that identifies a pattern of the numerical values, and determines a likelihood of the pattern. In an event that the likelihood is less than a threshold value, the quality assurance server flags the test plate as potentially contaminated, and in an event that the likelihood exceeds the threshold value, the quality assurance server refrains from flagging the test plate as potentially contaminated.

Abstract: A method for amplifying a target nucleic acid is disclosed, which includes: (a) fragmenting a nucleic acid sample to create a target fragment comprising a target nucleic acid and two probe-complementary portions; (b) contacting said fragmented nucleic acid sample with a probe comprising two target fragment-complementary portions complementary to the probe-complementary portions of the target fragment; (c) rendering the fragmented nucleic acid sample single-stranded; (d) allowing the probe-complementary portions to hybridise with the target-fragment complementary portions; (e) if the probe in step (b) is not immobilised, immobilising the probe-target fragment hybrid on a solid phase via immobilisation moiety; (f) separating non-immobilised nucleic acid fragments from the solid phase; (g) contacting the solid phase with a ligase to ligate ligatable 5? and 3? ends of the target fragment whereby the target fragment is circularized; and (h) amplifying said circularized target fragment.

Abstract: Provided herein, among other things, is a computer-implemented method for assigning a sequence read to a genomic location, the method including: a) accessing a file containing a sequence read, wherein the sequence read is obtained from a nucleic acid sample that has been enriched by hybridization to a plurality of capture sequences; and b) assigning the sequence read to a genomic location by: i) identifying a capture sequence as being a match with the sequence read if the sequence read contains one or more subsequences of the capture sequence; ii) calculating, using a computer, a score indicating the degree of sequence similarity between each of the matched capture sequences and the sequence read; and iii) assigning the sequence read to the genomic location if the calculated score for a matched capture sequence is above a threshold.

Abstract: The present invention provides a method for detecting or enriching for a target deoxyribonucleic acid (DNA) present in a nucleic acid sample, said method comprising: (a) fragmenting a nucleic acid sample to generate nucleic acid fragments including a target fragment containing said target DNA and non-specifically ligating an adaptor sequence to an end of said fragments; (b) rendering said fragments at least partially single-stranded; (c) contacting the at least partially single-stranded fragments of step (b) with oligonucleotides A and B of a single target-specific nucleic acid probe; (d) ligating oligonucleotide B of said probe to the part of the single-stranded portion of said target fragment which is hybridised to oligonucleotide A of said probe to produce a probe-target fragment hybrid; and (e) detecting or enriching for said probe-target fragment hybrid.

Abstract: A method for amplifying a target nucleic acid is disclosed, which includes: (a) fragmenting a nucleic acid sample to create a target fragment comprising a target nucleic acid and two probe-complementary portions; (b) contacting said fragmented nucleic acid sample with a probe comprising two target fragment-complementary portions complementary to the probe-complementary portions of the target fragment; (c) rendering the fragmented nucleic acid sample single-stranded; (d) allowing the probe-complementary portions to hybridise with the target-fragment complementary portions; (e) if the probe in step (b) is not immobilised, immobilising the probe-target fragment hybrid on a solid phase via immobilisation moiety; (f) separating non-immobilised nucleic acid fragments from the solid phase; (g) contacting the solid phase with a ligase to ligate ligatable 5? and 3? ends of the target fragment whereby the target fragment is circularized; and (h) amplifying said circularized target fragment.

Abstract: The present invention provides a method for detecting or enriching for a target deoxyribonucleic acid (DNA) present in a nucleic acid sample, said method comprising: (a) fragmenting a nucleic acid sample to generate nucleic acid fragments including a target fragment containing said target DNA; (b) rendering said fragments, including said target fragment, at least partially single-stranded, wherein the single-stranded portion includes an end portion and wherein the length of said single-stranded portion is sufficient to allow hybridisation of at least part of the single-stranded portion of said target fragment to the probe of step (c); (c) contacting the at least partially single-stranded fragments of step (b) with oligonucleotides A and B of a single target-specific nucleic acid probe, wherein: (i) oligonucleotide A is a single-stranded oligonucleotide comprising at one end a first target-specific part comprising at least 10 nucleotides complementary in sequence to at least part of said single-stranded portio