Abstract: The disclosure provides systems and methods for data analysis of experimental data. The analysis can include reference data that are not directly generated from the present experiment, which reference data may be values of the experimental parameters that were either provided by a user, computed by the system with input from a user, or computed by the system without using any input from a user. Another example of such reference data may be information about the instrument, such as the calibration method of the instrument.

Abstract: The present disclosure provides systems and methods for controllable protein generation. According to some embodiments, the systems and methods leverage neural network models and techniques that have been developed for other fields, in particular, natural language processing (NLP). In some embodiments, the systems and methods use or employ models implemented with transformer architectures developed for language modeling and apply the same to generative modeling for protein engineering.

Abstract: Techniques for predicting a protein sequence are described. An exemplary method includes receiving a request to predict a missing area of a protein's primary sequence and a corresponding three-dimensional position of the missing area; applying a machine learning model to backbone Cartesian coordinates of the protein's primary sequence and a protein vector of a representation of the protein's primary sequence including the missing area to predict a missing area of the protein primary sequence and a corresponding three-dimensional position for the missing area, wherein the machine learning model is selected from the group consisting of: an attention-based machine learning model, a bidirectional long short term memory-based model, and a convolutional neural network-based model; and outputting a result of the machine learning model.

Abstract: The present disclosure relates to Fragile X Syndrome (FXS) clinical testing, and in particular to an FXS AGG interruption polymerase chain reaction (PCR) assay and an AGG interruption genotyping algorithm for implementation into clinical testing. Particularly, aspects are directed to obtaining raw data from the FXS assay performed on a sample, iteratively searching the raw data and identifying one or more AGG peaks on the first allele using a first set of search spaces determined based on an expected AGG peak size, determining a number of CGG repeats downstream of a final AGG interruption and a number of CGG repeats preceding a first AGG interruption on the first allele based on the one or more AGG peaks, and generating an AGG genotype for the first allele based on the number of CGG repeats downstream of the final AGG interruption and the number of CGG repeats preceding the first AGG interruption.

Abstract: A method for characterizing a sample comprising genetic information, comprising: (i) receiving a plurality of sequencing signals from a sequencing operation for a sample, each of the plurality of sequencing signals representing a genetic sequence; (ii) setting, based on a received sequencing signal, a bit within a bit array to a first value for the received sequencing signal, wherein a set of one or more bits is associated with a unique received sequencing signal; (iii) calculating a rate of change of bits within the bit array as new sequencing signals are received; (iv) comparing the rate of change to a predetermined threshold; and (v) identifying the sequencing operation as insufficient if the rate of change is at or above the predetermined threshold, or identifying the sequencing operation as sufficient if the rate of change is at or below the predetermined threshold.

Abstract: A prenatal screening system includes a wet-laboratory arrangement and a data processing arrangement to exchange instructions and data with the wet-laboratory arrangement. The data processing arrangement includes a database arrangement storing genetic information accessible to one or more algorithms executable on the data processing arrangement. The wet-laboratory arrangement collects one or more maternal blood samples from a pregnant mother. The wet-laboratory arrangement isolates free fetal DNA fragments present in cell-free DNA derived from plasma of the one or more maternal blood samples. The isolation utilizes baits based upon coordinates of cell-free fetal DNA fragment specific end-points, and the data processing arrangement analyses the isolated free fetal DNA and compares with one or more DNA templates stored in the data processing arrangement for determining an occurrence of one or more biological characteristics of fetal DNA present in the one or more maternal blood samples.

Abstract: A method for designing a multi-objective primer pair is disclosed. The method includes inputting a DNA template fragment, a length of a forward primer, a length of a reverse primer, at least two objectives and optimal values for each of the at least two objectives to a computer system; generating, by the computer system, a plurality of primer pairs according to the DNA template fragment, the length of the forward primer and the length of the reverse primer; and calculating, by the computer system, numerical values of the at least two objectives of each of the plurality of primer pairs and inputting the numerical values of the at least two objectives of each of the plurality of primer pairs to a Pareto Chart tool to obtain at least one primer pair, and taking the primer pair as an optimal solution of the DNA template fragment.

Abstract: A genomic data analyzer maybe configured to detect and characterize biallelic genomic alterations for at least one gene in next generation sequencing variant calling information for patient tumor samples characterized by different purity ratios of somatic genomic material. The variant analysis module may compare the observed variant fraction distributions of putative heterozygous germline mutations to the theoretical distributions corresponding to different chromosomal aberration events to detect a combination of genomic alteration events. The variant analysis module maybe used in next-generation-sequencing oncogenomics testing to identify biallelic loss of function on tumor suppressor genes to facilitate the biological understanding and choice of a personalized oncology treatment targeting the analyzed patient tumor solely from next generation sequencing data variant information, without requiring complementary germline analysis or biological assays.

Abstract: A method of managing sequencing progress includes obtaining a plurality of samples and controlling a gene sequencing computing device to execute gene sequencing on the plurality of samples. Once a sequencing result is obtained by sending a query instruction to the gene sequencing computing device, sequencing information of the plurality of samples is displayed when a sequencing progress of the plurality of samples is determined to be meeting the preset condition according to the sequencing result.

Abstract: Methods for detecting a short genetic variant in a test sample are described herein. In some exemplary methods, the short genetic variant is called using one or more match scores, which are determined using one or more sequencing data sets obtained from a test nucleic acid molecule, wherein the test sequencing data sets are determined by sequencing the test nucleic acid molecule using non-terminating nucleotides provided in separate nucleotide flows according to a flow-cycle order. Also described herein are methods of sequencing a test nucleic acid molecule using two or more different flow-cycle orders and/or extended flow cycle orders having five or more nucleotide flows per flow cycle.