b'Reference | Support21.28. Can I use a different library quantification method or kit? Do I need to perform an adapter ligation prior to sequencingWe recommend using the KAPA kit for MiSeq assays andmy products?either the 2100 Bioanalyzer or the LabChip GX for the Ion S5/ Performing an adapter ligation is not needed. The primers PGM assays. included in our LymphoTrack and LymphoTrack Dx master mixes already include the appropriate index barcodes and adapter 22.Will the LymphoTrack or LymphoTrack Dx analysis softwaresequences. After PCR amplification, you will be able to proceedwork on my computer? with amplicon purification, amplicon quantification, library The software requires Microsoft Windows 7 (64-bit) and Excelpooling, and sequencing.2007, 2010, or 2013 and will work with most desktop or laptop29.If the LymphoTrack or LymphoTrack Dx software generated an PCs. For specific requirements please refer to the software instructions for use.error, what information should I submit to Technical Support?Please submit the *.txt Log file that should have been created by the software in the output folder, a screenshot of the sample23.Can I use the LymphoTrack or LymphoTrack Dx bioinformaticsdirectory, and the Lot Number of the software CD you are using software with a different assay? to support@invivoscribe.com.No, the software will only work with datasets obtained by our30.Are controls provided with the kits? Can you purchase LymphoTrack and LymphoTrack Dx Assays.additional controls? How are they supplied?24.What characters can I use when naming my samples andEach kit contains the necessary positive and negative controlsthe file pathways? What types of files are accepted by therequired to perform the assay; additional controls may also be LymphoTrack and LymphoTrack Dx Software - MiSeq? purchased separately. Single-tube DNA controls are provided Our software only recognizes file names and pathways thatas 100 L aliquots of 200 g/mL in 1/10 TE Buffer, 50 L aliquots contain the following characters (A-Z, a-z, 0-9, . (dot), _of 50 g/mL in 1/10 TE Buffer, and 45 L aliquots of 15 g/mL in (underscore), - (hyphen)). In addition, spaces in the pathname1/10 TE Buffer. Single-tube RNA controls are provided as 100 L for the data files or software (pathnames include file foldersaliquots of 400 g/ml in RNAse free in glass distilled water.and file names) should be avoided. If the software encounters31.What are the differences between dilution sets, sensitivity panels, a character that is not listed above or extra spaces, an error message may be generated. Furthermore, the software isand proficiency panels?only compatible with adaptor-trimmed fastq.gz files that are31a.RNA Dilution Sets generated by the MiSeq Reporter Software when the MiSeqBCR/ABL b3a2 (Cat# 4-085-0210), BCR/ABL b2a2 (Cat# instrument is used. An example of the naming format that the4-085-0310), and BCR/ABL e1a2 (Cat# 4-085-0110). These MiSeq Reporter uses: SampleName_S1_L001_R1_001.fastq.gzsets contain six tubes: 100% negative control RNA and and SampleName_S1_L001_R2_001.fastq.gz. volume to volume (v/v) dilutions (10- 1 , 10- 2 , 10- 3 , 10- 4 , and 10- 5 ) of the positive control RNA into the negative control 25.Do the Invivoscribe MiSeq indices correspond to the RNA (IVS-0048). The RNA Dilution Sets are supplied atIllumina indices? a concentration of 400 g/mL, and each tube contains The indices included in our MiSeq master mixes follow50 L. These dilution sets may be used to establish a Illuminas TruSeq LT nomenclature. For instance, IGH FR1standard reference curve, as proficiency controls, as MiSeq 01 corresponds to A001. Information for the other indicessensitivity controls for specific target assays, and as can be found in the instructions for use on how to set up theroutine testing controls for cDNA synthesis, amplification MiSeq Sample Sheet to detect the appropriate indices. and detection.26.31b.RNA Sensitivity PanelsWhy am I getting a low percent passing filter and Q30 score? These panels consist of seven tubes: 100% positive control Low Q30 and percent passing filter (%PF) scores couldRNA and v/v dilutions (10- 1 , 10- 2 , 10- 3 , 10- 4 , 10- 5 , and 10- 6 ) be an indication that the flow cell is overloaded. If this isof the positive control RNA into the negative control RNA suspected, verify your amplicon and library calculations(IVS-0035). The RNA Sensitivity Panels are supplied at a and quantifications are correct. Low run metrics can also beconcentration of 400 g/mL, and each tube contains 100 attributed to many additional factors including poor qualityL. The RNA Sensitivity Panels may be used as sensitivity DNA, contamination, flow cell or instrument issues, etc. Pleasecontrols for specific target assays, and as routine testing refer to your Illumina MiSeq user guides and contact Illuminacontrols for cDNA synthesis, amplification and detection.Support.31c. DNA Sensitivity Panels27.H -J Hrearrangement combination andConsist of six tubes: 100% clonal DNA and v/v dilutions of the Why is the same Vsequence shared by two groups of reads, one of which is severalclonal DNA into negative polyclonal DNA (IVS-0000) to make bases shorter than the other when looking at the Read Summary30%, 20%, 10%, 5%, and 1% dilutions. The DNA Sensitivity Panels tab of the excel document created by the LymphoTrackare supplied at a concentration of 200 g/mL and each tube Visualization Tool? contains 100 L. The DNA Sensitivity Panels may be used as Our software was designed to list every unique sequencesensitivity controls for specific target assays.separately in order for the customer to see all of the data and31d.RNA Proficiency Panel make their own determination on how to interpret it. The severalThe proficiency panel for BCR-ABL1 t(9;22) can be used base pair difference can be due to a number of factors includingas a sensitivity control for specific target assays, and as amplification errors and sequencing errors. It could also be aroutine testing controls for cDNA synthesis, amplification result of similarities between some of the primer sequences thatand detection. It consists of ten tubes: 100% positive control were designed to ensure maximum coverage. We also include aRNA and v/v dilutions (10- 2and 10- 4 ) of IVS-0003, IVS-0011 Merged Read Summary report for your reference that combinesand IVS-0032. It also includes BCR-ABL1 Negative Clonal sequences that only differ by 1 or 2 basepairs. Control RNA (IVS-0035).160'