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Thread: Long Read Chromium Whole Genome Product

  1. #1
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    Long Read Chromium Whole Genome Product

    The Long read chromium test yields phased data and includes structural variants. The short read (i.e. 30x whole genome) does not yield phased data. The long read is useful if you are doing special medical testing or you want the best coverage of the Y chromosome for ancestry.
    20 mb Chromium
    14 mb Y Elite
    9.3 mb Big Y

    See article:
    "Standard short read sequencing provides accurate base level sequence to provide short range information, but struggles to provide long range information. This means that standard sequencing and analysis approaches typically do well at calling single nucleotide variants (SNVs) but fail to robustly identify the full spectrum of structural variation seen in an individual genome. A novel data type known as Linked-Reads utilizes molecular barcodes to tag reads that come from the same long DNA fragment.



    Linked-Reads provide the long range information missing from standard approaches. By adding a unique barcode to every short read generated from an individual molecule, you can link the short reads together."

    https://community.10xgenomics.com/t5...-reads/ba-p/95
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    From our analyst, Greg Magoon:

    The raw reads from the Chromium sequencing are still only 2x151 bp (Illumina platform), but the barcoding used by the approach enables linking reads from much larger parent DNA fragments, around say 40 kbp. So the linked reads (sometimes called "read clouds") enable significant improvements to mapping, phasing, and structural variant identification. One of the biggest advantages of this approach over current long-read platforms (e.g. Oxford Nanopore and Pacific Biosciences) is that it doesn't suffer from the high error rate associated with those technologies.
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    https://www.10xgenomics.com/solution...CAAEgJbIvD_BwE

    Call and phase major classes of structural variants (SVs) like deletions, inversions, and translocations, even in genes inaccessible to short-read sequencers
    Phase SNVs, indels and SVs across >10 Mb haplotype blocks
    From the manufacturer, 10x Genomics
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    Screen Shot 2018-09-13 at 5.33.54 PM.png

    Long read statistics vs 30x whole genome
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    Another long read Chromium result:

    Y coverage for a Long Read Chromium
    20,578,879 loci

    In comparison:
    Y Elite: 14,000,000 loci
    Big Y: 9,300,000 loci
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    I ordered my FGC long read Chromium test in March 2018, received the results at the end of July. My tests results are now available to the public. This Google Drive folder contains test results from various labs, the FGC Long Read results are in subfolder 9LSKM.
    https://drive.google.com/drive/folde...F3?usp=sharing
    Included are the vcf and fastq files, there is a bam file for the Y chromosome only at the moment. Please feel free to take a look at those if you're considering taking the test or are waiting for your results and are wondering what you might get back - or for any other purpose.

  10. The Following 5 Users Say Thank You to pmokeefe For This Useful Post:

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    Quote Originally Posted by pmokeefe View Post
    I ordered my FGC long read Chromium test in March 2018, received the results at the end of July. My tests results are now available to the public. This Google Drive folder contains test results from various labs, the FGC Long Read results are in subfolder 9LSKM.
    https://drive.google.com/drive/folde...F3?usp=sharing
    Included are the vcf and fastq files, there is a bam file for the Y chromosome only at the moment. Please feel free to take a look at those if you're considering taking the test or are waiting for your results and are wondering what you might get back - or for any other purpose.
    Thanks, are you able to offer a comparison between Y variant detection on this compared with any prior tests either with FGC or elsewhere? Anything found eg new types of variant that would require the LR technology to detect? Extra SNPs or STRs that other tests didn't read?
    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
    WGS (Full Genomes Nov 2015, YSEQ Feb 2019, Dante Mar 2019, FGC-10X Linked Reads Apr 2019, Dante-Nanopore May 2019) - further WGS tests pending ;-)
    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
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    FBIMatch: A828783 (autosomal DNA) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT

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    9LKSM is the same donor as 15001710504417A on haplogroup-r.org. The much longer kit# is Dante Labs 30x WGS. The tree entrees show 7 unshared mutations in each test, which I haven't had time to chase down to see if they are just alignment issues in the Dante test. The close proximity of half of them would strongly indicate that though.

    The many of his FLR named variants have been seen in other non-Big Ys, but I'm also sure my tool chain scraped quite a few in 9LKSM and the 5 other Long Read tests. For raxml to play well with data sets, all the locations not sampled in at least 90% of the cohort with at least 13 million base pairs called must be excluded. On the positive side it's hinting at a new layer of branching at FGC40956 under R-Z16252 that the O'Keefe share with the O'Moriarty and O'Donoghue lines from southern Ireland.

  14. The Following 3 Users Say Thank You to JamesKane For This Useful Post:

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    Quote Originally Posted by MacUalraig View Post
    Thanks, are you able to offer a comparison between Y variant detection on this compared with any prior tests either with FGC or elsewhere? Anything found eg new types of variant that would require the LR technology to detect? Extra SNPs or STRs that other tests didn't read?
    I currently don't have much information beyond what James Kane just provided. The kit number for my Dante Labs test on Yfull is YF14620, but I have not submitted my FGC Long Read results there. I believe FGC can also provide Y analysis, but I haven't received those yet (due to circumstances, not at all their fault). I just requested that from FGC and will post those when I receive them.

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  17. #10
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    At 39 minutes, 57 seconds there is a discussion of FGC's long read test in this presentation:
    https://www.youtube.com/watch?v=SJnI8I9WitE&t=2814s

    There is one point that is worth mentioning. The test yields up to 40% or more data than Y Elite. Also, the yield will improve even more with new analytical approaches.
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