Deze informatie over BNGO werd gepost op het Yahoo Message Board. 90% van de posts daar t.a.v. aandelen zijn niet interessant, maar deze wel:
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[Basic scientist with 30 years experience in molecular biology here] Entering the discussion here as I've observed an unfortunate misapprehension by those on either side of the Bionano Genomics debate. That is the mistaken belief that Bionano has somehow fallen short of the mark because the performance spectrum of their Saphyr platform operates most efficiently at SV 500 bp>. Accordingly, some have pointed to Pac Bio's SMRT sequencing approach -- wherein their tool's discernment works best with SV's < 500 bp.
Thus, the fallacy seems to surmise that Bionano constitutes a less precise, and therefore less useful tool. I'll not enter into an exhaustive disquisition on the nano scale-landscape as the operative differentials are esoteric even for many MD clinicians. But let me just note that from a bioinformatics standpoint, Bionano's OM system constitutes a true paradigm shift that will soon affect multiple realms of science and medicine.
Let's shed light by giving the discussion some useful context.
From the middle of the past century until now, the state of art has been population based and akin to 'shotgun medicine'. Therefore, as we all know, a broad spectrum antimicrobial works against numerous pathogenic organisms -- but also tends to decimate one's microbiome.
Tools such as Saphyr will be part of the transformation from population based to individual based treatment, and the development of targeted /sniper bullet' therapies. It is now widely understood that this revolution will directly and substantively change medicine as we know it. From infectious disease, to ameliorating the impediments of aging, to the treatment of cancer, the new targeted therapies will be designed specifically for the individual and thus will work far more effectively, efficiently -- and with far fewer negative side effects.
Particularly exciting are the new possibilities in addressing heretofore refractory genetic susceptibilities and complex trait disorders where structural variants both <500 bp and 500 bp> occur. Here, a confluence of bioinformatics and dynamic modulation (e.g. crispr) will identify risk factors, localize their genomic locale and edit or ablate them as needed. This has resonance in the treatment of birth defects such as mitochondriopathies, lysosomal storage diseases etc.
By the end of next week a number of quite remarkable proof-of-principle success (rescue of phenotype) stories will have been presented by Bionano. My hope is that those invested in this company will come to recognize that they're quite literally contributing to bringing forward one of the most salutary advances of our time.
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A number of folks have raised two interrelated questions that are actually quite important in comprehending the key variables. To paraphrase, [...what's the difference between short and long sequences?] and [...what are the advantages of OM (optical mapping) over conventional sequencing techniques?]
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So to begin, short read sequencing (SRS), once the Gold standard in genome analytics, remains useful but is also linked to a number of inherent challenges; particularly arising when attempting to analyze long strands of DNA. Let me cite an imperfect analogy. Imagine trying to read and use a recipe after all the words have been cut into pieces, duplicated and rearranged. Wouldn't you prefer one where some semblance of the natural order is preserved? This, in essence is the task facing those charged with extrapolating relevant data from small variant sequence throughput. Having spent far too many years engaged in the process I can assure you it can be quite the challenge to make sense of all the scrambled pieces.
However, for a very long time, SRS was all there was.
This brings us to optical mapping.
Advantages of optical mapping (OM), -as found in the Bionano system- are manifold. But among the top three are the following.
1: Ease of comprehension -- OM permits the preservation of the order of each polymorphic sequence resulting in a greater degree of read-confidence. This is one key data point you can mention in retort to those 'clever' souls who stubbornly insist that short read SV throughput (<500 bp) is inherently superior to Bionano's new OM approach.
2: Cost -- Since only a relatively minuscule DNA sample is needed, the cumbersome and cost-intensive step of amplification is obviated.
3: Speed -- DNA barcoding provides for remarkably rapid, thorough and specific analysis.
NOTE: This is, of course, not to imply that OM shall necessarily eclipse Pac Bio’s SMRT sequencing entirely. There will continue to be many occasions when the SMRT approach will offer useful advantage. It is also likely that OM and SMRT may soon be found to work best in combination. Thus, it is probably most accurate to recognize a place exists for both discernment methodologies, each filling a crucial role in furthering the advance of the Bio-Informatics revolution.