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: Systems, platforms, methods and media for providing genomic services are disclosed. In one example, a genomic services platform comprises a network interface through which are received genomic sequence reads derived from a biological sample obtained from a user The platform also includes a bioinformatics processing pipeline including a read alignment module configured to generate observed sequence data by aligning the sequence reads relative to a reference sequence, a variant calling module operative to identify observed variants in the observed sequence data, and a variant refinement module for producing a set of refined variants associated with the user. A variant imputation module produces a set of imputed variants associated with the user, and a variant storage module disposed to receive a query from network infrastructure of a partner application provider and to provide selected ones of the refined or imputed variants in response to the query.

Abstract: Systems, platforms, methods and media for providing genomic services axe disclosed. In one example, a system for providing genomic services comprises genomic sequencing equipment configured to generate sequence reads based upon a biological sample obtained from a user, store the sequence reads in a FASTQ storage file, and communicate the FASTQ file electronically to a recipient. The system also includes a genomic services platform which includes a network interface through which the sequence reads are received, and a bioinformatics processing pipeline. The bioinformatics processing pipeline includes a read alignment module configured to generate observed sequence data, and a variant calling module is operative to identify observed variants in the observed sequence data. A variant storage module is disposed to receive a query from network infrastructure of a partner application provider and to provide selected ones of refined variants in response to a query.

Abstract: Systems, platforms, methods and media for providing genomic services are disclosed. In one example, a genomic services platform comprises a network interface through which are received genomic sequence reads derived from a biological sample obtained from a user. The platform also includes a bioinformatics processing pipeline including a read alignment module configured to generate observed sequence data by aligning the sequence reads relative to a reference sequence, a variant calling module operative to identify observed variants in the observed sequence data, and a variant refinement module for producing genotype data including a set of refined variants associated with the user. A variant imputation module produces a set of imputed variants associated with the user, and is configured to receive, as input, at least some of the genotype data and separate the genotype data into high-quality and low-quality genotypes based on a genotype quality.

Abstract: Systems, platforms, methods and media for providing genomic services are disclosed. In one example, a genomic services platform comprises a network interface through which genomic sequence reads derived from a biological sample obtained from a user are received. The platform also includes a bioinformatics processing pipeline that includes a read alignment module configured to receive a genomics file from genomic sequencing equipment and use data contained therein to generate observed sequence data by aligning the sequence reads relative to a reference sequence. A variant calling module identifies observed variants in the observed sequence data and stores the observed variants in a variant calling file. A variant refinement module produces genotype data including a set of refined variants associated with the user, and a variant imputation module produces a set of imputed variants associated with the user.

Abstract: Systems, platforms, methods and media for providing genomic services are disclosed. In one example, a genomic services platform comprises a network interface through which are received genomic sequence reads derived from a biological sample obtained from a user The platform also includes a bioinformatics processing pipeline including a read alignment module configured to generate observed sequence data by aligning the sequence reads relative to a reference sequence, a variant calling module operative to identify observed variants in the observed sequence data, and a variant refinement module for producing a set of refined variants associated with the user. A variant imputation module produces a set of imputed variants associated with the user, and a variant storage module disposed to receive a query from network infrastructure of a partner application provider and to provide selected ones of the refined or imputed variants in response to the query.

Abstract: Systems, platforms, methods and media for providing genomic services are disclosed. In one example, a platform comprises a network interface, in communication with a sequencing laboratory, through which are received genomic sequence reads derived from a biological sample obtained from a user, and a bioinformatics processing pipeline. The pipeline includes a read alignment module configured to generate observed sequence data by aligning the sequence reads relative to a reference sequence, a variant calling module operative to identify observed variants in the observed sequence data, a genomic data storage containing at least the observed variants in the observed sequence data, and a variant storage module disposed to receive a query from network infrastructure of a partner application provider and to provide genomic information based on or derived from the observed variants in response to the query.

Abstract: Systems, platforms, methods and media for providing genomic services are disclosed. In one example, a genomic services platform comprises a network interface through which genomic sequence reads derived from a biological sample are received. The platform also includes a bioinformatics processing pipeline that comprises a read alignment module configured to generate observed sequence data by aligning the sequence reads relative to a reference sequence, a variant calling module operative to identify observed variants in the observed sequence data, and a variant refinement module for producing a set of refined variants associated with the biological sample. A variant imputation module produces a set of imputed variants associated with the user and a variant storage module, operating on a server-less framework, is disposed to receive a query from network infrastructure of a partner application provider and to provide selected ones of the refined or imputed variants m response to the query.

Abstract: Methods, systems and media for providing genomic services are disclosed. In one example, a system comprises genomic sequencing equipment configured to generate sequence reads based upon a biological sample obtained from a user, and a genomic services platform. The platform includes a network interface through which the sequence reads are received. A bioinformatics processing pipeline includes a read alignment module configured to generate observed sequence data by aligning the sequence reads relative to a reference sequence, and a variant calling module is operative to identify observed variants in the observed sequence data. Genomic data storage contains the observed variants in the observed sequence data. A variant storage module is disposed to receive a query from network infrastructure of a partner application provider and to provide genomic information based on or derived from the observed variants in response to the query.

Abstract: Systems, platforms, methods and media for providing genomic services are disclosed. In one example, a genomic services platform comprises a network interface through which are received genomic sequence reads derived from a biological sample obtained from a user. The platform also includes a bioinformatics processing pipeline including a read alignment module configured to generate observed sequence data by aligning the sequence reads relative to a reference sequence, a variant calling module operative to identify observed variants in the observed sequence data, and a variant refinement module for producing genotype data including a set of refined variants associated with the user. A variant imputation module produces a set of imputed variants associated with the user, and is configured to receive, as input, at least some of the genotype data and separate the genotype data into high-quality and low-quality genotypes based on a genotype quality.

Abstract: Methods, systems and media for providing genomic services are disclosed. In one example, a system for providing genomic services comprises genomic sequencing equipment configured to generate sequence reads based upon a biological sample obtained from a user, and a genomic services platform. The platform includes genomic data storage containing observed sequence data generated by aligning the sequence reads relative to a reference sequence and variants in the observed sequence data derived from the observed sequence data. File storage includes one or more files defining one or more genomic windows respectively associated with each of a plurality of partner application providers or partner applications.