b'Next-Generation Sequencing (NGS) | CE-IVD AssaysBioinformatics Software Next-Generation Sequencing (NGS) | CE-IVD Assays Bioinformatics Software Next-Generation Sequencing (NGS) | CE-IVD AssaysLymphoTrack Dx Bioinformatics Software Sequencing SummaryUsing the merged read summary, along with the easy to follow flow charts in the accompanying LymphoTrack Dx Assay instructions for use (IFU), interpretation is quick and easy.Software UseThe LymphoTrack Dx Bioinformatics Software package is providedSample Namewith each LymphoTrack Dx Assay to analyze raw FASTQ files for1clonality analysis of single or multiple target data sets (IGHV Leader,Total reads = 32,458IGH FR1, IGH FR2, IGH FR3, IGK, TRB, or TRG). For data generated with2 3 4 5LymphoTrack Dx IGHV Leader or IGH FR1 Assays, the software provides additional information, including the rate of somatic hypermutationMerge% TotalCumulative Mutation rate In-frameNo stop and whether a clone would be functional based upon the presenceRank Sequence Length count V-gene J-gene reads %partial V-gene(Y/N) codon V-coverageof a premature stop codon. The software can also predict whether an(%) (Y/N)open reading frame would be in- or out-of-frame.1 TTCTCGTGGTG 455 29603 IGHV4-59_08 IGHJ4_02 9.93 9.93 11.26 Y Y 98.63The provided software is composed of two distinct parts:2 CTCGCCCTCCT 463 205 IGHV5-51_01 IGHJ4_02 0.07 9.99 0.00 Y Y 99.661.A bioinformatics Data Analysis Application3 GGTTTTCCTTG 484 201 IGHV3-7_01 IGHJ4_02 0.07 10.06 7.77 Y Y 100.002. Microsoft Excel Data Visualization spreadsheets and automated4 CTCGCCCTCCT 463 185 IGHV5-51_01 IGHJ5_02 0.06 10.12 6.08 Y Y 99.32Sample-to-PDF Reports for streamlined data analysis for VJ usage 5 CTCGCCCTCCT 469 170 IGHV5-51_01 IGHJ4_02 0.06 10.18 0.00 Y Y 99.32and VJ sequence frequency graphs.6 CTCGCCCTCCT 466 160 IGHV5-51_01 IGHJ4_02 0.05 10.23 0.00 Y Y 99.667 CTGCTGCTGAC 460 159 IGHV2-5_10 IGHJ5_02 0.05 10.29 8.08 Y Y 97.648 GGTTTTCCTTG 493 156 IGHV3-48_02 IGHJ6_02 0.05 10.34 3.72 Y Y 98.999 CTCGCCCTCCT 334 153 IGHV5-51_02 IGHJ2_01 0.05 10.39 3.72 Y N 27.7010 CTCGCCCTCCT 334 152 IGHV5-51_02 IGHJ2_01 0.05 10.44 3.38 Y N 26.01Sequence Frequency Graph 1. The sample name is clearly identified and the total number of reads (= Read Depth) generated for the sample is provided. Following 1the IFU, it is easy to determine whether the data generated for a sample can be assessed for the presence or absence of clonality.LymphoTrack IGH Assay - V - J Sequence FrequenciesLymphoTrack Dx IGH Assay - V - J Sequence Frequencies 2.The sequence of clonal populations is provided and populations are ranked from most abundant to least prevalent. Sequences LymphoTrack IGH Assay -V J Sequence Frequencies 26 that differ by 1-2 basepairs are automatically merged to account for possible sequencing errors and to improve the accuracy and ease of sample interpretation.3.Sequences are aligned with reference genes to allow for easy identification of specific types of gene rearrangements such as IGHV3-21,35 Unique sequence which is characteristic of some CLL cases and correlates with a poor prognosis.CATCTGGATACACCTTCACCAGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGG4.The percentage that a unique sequence contributes to the total number of reads for a sample is calculated. Following the guidelines in the 4GCTTGAGTGGATGGGAATAATCAACCCTAGTGGTGGTAGCACAAGCTACGCACAGAAGTTCC 4 AGGGCAGAGTCACCATGACCAGGGACACGTCCACGAGCACAGTCTACATGGAGCTGAGCAGIFU, samples can be interpreted for the evidence indicating the presence or absence of clonality.CCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCTAGAGATCTCACAGGTTGTATTAGT5. For the LymphoTrack Dx IGHV Leader and IGH FR1 Assays, the somatic hypermutation status of a sequence is automatically calculated by ACCAGCTGCTATCCTCCGAACTACTTTGACTACTGGGGCCAGGGAACCCT 5 comparing the identified sequence with a germline reference. In addition, predictions on whether the sequence would be functional can be % Total Reads % Total Readsdrawn by the provided information regarding the presence of a premature stop codon or an open reading frame that is out-of-frame.3 Gene rearrangement familyIGHV1-46_03 -IGHJ4_02 2Ordering InformationCatalog # Products Quantity Components19-500-0009 LymphoTrack Dx Software - MiSeq 1 CD complimentary with kit purchase9-500-0007 LymphoTrackDx Software - S5/PGM 1 CD complimentary with kit purchase0The stacked bar graph depicts the top 200 sequencing reads for a sample. Each individual colored bar represents a unique population of cells. Different colors stacked at the same point on the x-axis represent unique sequences that utilize the same V and J gene families. The amplicons of these products vary in sequence and may also vary in product size. These products are CE-IVD assays for in vitro diagnostic use.36Invivoscribe 2021|37'