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> <channel><title>Comments for Genomes Unzipped</title> <atom:link href="http://www.genomesunzipped.org/comments/feed" rel="self" type="application/rss+xml" /><link>http://www.genomesunzipped.org</link> <description>public personal genomics</description> <lastBuildDate>Thu, 23 Feb 2012 00:32:11 +0000</lastBuildDate> <sy:updatePeriod>hourly</sy:updatePeriod> <sy:updateFrequency>1</sy:updateFrequency> <generator>http://wordpress.org/?v=3.3.1</generator> <item><title>Comment on Making sequencing simpler with nanopores by The Three Musketeers of Genome Sciences and Bioinformatics &#171; Aakhayan</title><link>http://www.genomesunzipped.org/2012/02/making-sequencing-simpler-with-nanopores.php#comment-201474</link> <dc:creator>The Three Musketeers of Genome Sciences and Bioinformatics &#171; Aakhayan</dc:creator> <pubDate>Thu, 23 Feb 2012 00:32:11 +0000</pubDate> <guid
isPermaLink="false">http://www.genomesunzipped.org/?p=4385#comment-201474</guid> <description>[...] The scientific landscape is gradually changing from a hypothesis-driven science to a data-driven science. Since the introduction of the 454 Pyrosequencing technology in 2005, which marked the beginning of the Next Generation Sequencing (NGS) era, bioinformaticians have been inundated with sequencing data. Few days back, on 17th Feb 2012, a ground breaking sequencing technology by Oxford Nanopore was announced in the Advances in Genome Biology and Technology (AGBT) conference. It was a big buzz all over the popular social media and this morning everyone in our department was talking about it. A miniaturized sequencing device called MinION, which is  just like a USB flash drive in terms of size and shape, will just put the cost of sequencing to $900. This breakthrough can put genome sequencing right to the doctor’s table within the beginning of next year and revolutionize the way we deliver health-care. But on the other hand, it will further sky-rocket the sequence data volume into an unimaginable height (Blogs on MiniON: Pathogens: Genes and Genomes; genomes unzipped). [...]</description> <content:encoded><![CDATA[<p>[...] The scientific landscape is gradually changing from a hypothesis-driven science to a data-driven science. Since the introduction of the 454 Pyrosequencing technology in 2005, which marked the beginning of the Next Generation Sequencing (NGS) era, bioinformaticians have been inundated with sequencing data. Few days back, on 17th Feb 2012, a ground breaking sequencing technology by Oxford Nanopore was announced in the Advances in Genome Biology and Technology (AGBT) conference. It was a big buzz all over the popular social media and this morning everyone in our department was talking about it. A miniaturized sequencing device called MinION, which is  just like a USB flash drive in terms of size and shape, will just put the cost of sequencing to $900. This breakthrough can put genome sequencing right to the doctor’s table within the beginning of next year and revolutionize the way we deliver health-care. But on the other hand, it will further sky-rocket the sequence data volume into an unimaginable height (Blogs on MiniON: Pathogens: Genes and Genomes; genomes unzipped). [...]</p> ]]></content:encoded> </item> <item><title>Comment on Is industry best practice in DTC genetics good enough? by fat tuesday</title><link>http://www.genomesunzipped.org/2010/07/is-best-practice-in-dtc-genetics-good-enough.php#comment-201423</link> <dc:creator>fat tuesday</dc:creator> <pubDate>Wed, 22 Feb 2012 22:56:04 +0000</pubDate> <guid
isPermaLink="false">http://www.genomesunzipped.org/?p=567#comment-201423</guid> <description>Thanks for your post. I&#039;d really like to comment that the cost of car insurance differs a lot from one policy to another, given that there are so many different facets which bring about the overall cost. As an example, the brand name of the motor vehicle will have an enormous bearing on the purchase price. A reliable ancient family automobile will have a more affordable premium compared to a flashy expensive car.</description> <content:encoded><![CDATA[<p>Thanks for your post. I&#8217;d really like to comment that the cost of car insurance differs a lot from one policy to another, given that there are so many different facets which bring about the overall cost. As an example, the brand name of the motor vehicle will have an enormous bearing on the purchase price. A reliable ancient family automobile will have a more affordable premium compared to a flashy expensive car.</p> ]]></content:encoded> </item> <item><title>Comment on Guest post: Time to bring human genome sequencing into the clinic by Ülo</title><link>http://www.genomesunzipped.org/2012/02/guest-post-time-to-bring-human-genome-sequencing-into-the-clinic.php#comment-201362</link> <dc:creator>Ülo</dc:creator> <pubDate>Wed, 22 Feb 2012 20:36:41 +0000</pubDate> <guid
isPermaLink="false">http://www.genomesunzipped.org/?p=4357#comment-201362</guid> <description>If I understand correctly, ogden syndrome is a recessive x-linked disease for which the authors knew that the maternal grandmother of the male fetus was a carrier. If the mother knows that she is a carrier also, her probability of giving birth to a sick boy is 50%. On the other hand, if the mother does not have this information her subjective probability is 25% and if the mother knows for sure that she is not a carrier the probability approaches zero.
The expert choose to withhold information from the mother leaving her with the subjective probability of 25% of having a sick baby. The question now becomes this: what was the true level of knowledge of the expert (as opposed to the mother)? Lets suppose that the probability of the test showing a mutation in the right position when this position is in fact wild-type is 5% (a fairly sloppy research scientist might be assumed to mislabel or otherwise mix up 1 test tube in 20, sequencing error-rate must be much lower). Lets further suppose that the probability of the test outcome being &quot;wild-type&quot; when the mother is in fact a mutation carrier is also 5%.
Using the Bayes rule we can calculate that the expert should now believe with 95% certainty that the mother is a carrier.
If the expert believed that only 1% error-rate applies, then the level of his belief should rise to 99%.
The mother may know very little about genetics but this is surely not a valid reason to deprive her of the chance of interpreting the statement: „it is over 95% probable that your baby boy will have a fifty-fyfty chance of having the disease“? Or put differently: would it be a good idea to wait several months in order to be able instead to say: „it is over 99,9% probable that your baby boy will have a 50:50 chance of being sick“? It seems doubtful to me that the difference between 95% and 99,9% would be enough to change the mother‘s behaviour.</description> <content:encoded><![CDATA[<p>If I understand correctly, ogden syndrome is a recessive x-linked disease for which the authors knew that the maternal grandmother of the male fetus was a carrier. If the mother knows that she is a carrier also, her probability of giving birth to a sick boy is 50%. On the other hand, if the mother does not have this information her subjective probability is 25% and if the mother knows for sure that she is not a carrier the probability approaches zero.</p><p>The expert choose to withhold information from the mother leaving her with the subjective probability of 25% of having a sick baby. The question now becomes this: what was the true level of knowledge of the expert (as opposed to the mother)? Lets suppose that the probability of the test showing a mutation in the right position when this position is in fact wild-type is 5% (a fairly sloppy research scientist might be assumed to mislabel or otherwise mix up 1 test tube in 20, sequencing error-rate must be much lower). Lets further suppose that the probability of the test outcome being &#8220;wild-type&#8221; when the mother is in fact a mutation carrier is also 5%.</p><p>Using the Bayes rule we can calculate that the expert should now believe with 95% certainty that the mother is a carrier.<br
/> If the expert believed that only 1% error-rate applies, then the level of his belief should rise to 99%.</p><p>The mother may know very little about genetics but this is surely not a valid reason to deprive her of the chance of interpreting the statement: „it is over 95% probable that your baby boy will have a fifty-fyfty chance of having the disease“? Or put differently: would it be a good idea to wait several months in order to be able instead to say: „it is over 99,9% probable that your baby boy will have a 50:50 chance of being sick“? It seems doubtful to me that the difference between 95% and 99,9% would be enough to change the mother‘s behaviour.</p> ]]></content:encoded> </item> <item><title>Comment on Guest post: Time to bring human genome sequencing into the clinic by Genomes Unzipped Posting &#171; utahresearch.org</title><link>http://www.genomesunzipped.org/2012/02/guest-post-time-to-bring-human-genome-sequencing-into-the-clinic.php#comment-201247</link> <dc:creator>Genomes Unzipped Posting &#171; utahresearch.org</dc:creator> <pubDate>Wed, 22 Feb 2012 14:50:35 +0000</pubDate> <guid
isPermaLink="false">http://www.genomesunzipped.org/?p=4357#comment-201247</guid> <description>[...] http://www.genomesunzipped.org/2012/02/guest-post-time-to-bring-human-genome-sequencing-into-the-cli...   [+] Share &amp; Bookmark   &#8226; Twitter  &#8226; StumbleUpon  &#8226; Digg  &#8226; Delicious  &#8226; Facebook [...]</description> <content:encoded><![CDATA[<p>[...] <a
href="http://www.genomesunzipped.org/2012/02/guest-post-time-to-bring-human-genome-sequencing-into-the-cli.." rel="nofollow">http://www.genomesunzipped.org/2012/02/guest-post-time-to-bring-human-genome-sequencing-into-the-cli..</a>.   [+] Share &amp; Bookmark   &#8226; Twitter  &#8226; StumbleUpon  &#8226; Digg  &#8226; Delicious  &#8226; Facebook [...]</p> ]]></content:encoded> </item> <item><title>Comment on Making sequencing simpler with nanopores by The Three Musketeers of Genome Sciences and Bioinformatics &#124; TalkBiotech</title><link>http://www.genomesunzipped.org/2012/02/making-sequencing-simpler-with-nanopores.php#comment-201213</link> <dc:creator>The Three Musketeers of Genome Sciences and Bioinformatics &#124; TalkBiotech</dc:creator> <pubDate>Wed, 22 Feb 2012 13:19:52 +0000</pubDate> <guid
isPermaLink="false">http://www.genomesunzipped.org/?p=4385#comment-201213</guid> <description>[...] The scientific landscape is gradually changing from a hypothesis-driven science to a data-driven science. Since the introduction of the 454 Pyrosequencing technology in 2005, which marked the beginning of the Next Generation Sequencing (NGS) era, bioinformaticians have been inundated with sequencing data. Just a few days back, on February 17, 2012, a ground breaking sequencing technology by Oxford Nanopore was announced in the Advances in Genome Biology and Technology (AGBT) conference. It was a big buzz all over the popular social media and that morning everyone in our department was talking about it. A miniaturized sequencing device called MinION, which just like a USB flash drive in terms of size and shape, will just put the cost of sequencing to $900. This breakthrough can put genome sequencing right to the doctor’s table within the beginning of next year and revolutionize the way we deliver health-care. But on the other hand, it will further sky-rocket the sequence data volume into an unimaginable height (Blogs on MinION: Pathogens: Genes and Genomes; genomes unzipped). [...]</description> <content:encoded><![CDATA[<p>[...] The scientific landscape is gradually changing from a hypothesis-driven science to a data-driven science. Since the introduction of the 454 Pyrosequencing technology in 2005, which marked the beginning of the Next Generation Sequencing (NGS) era, bioinformaticians have been inundated with sequencing data. Just a few days back, on February 17, 2012, a ground breaking sequencing technology by Oxford Nanopore was announced in the Advances in Genome Biology and Technology (AGBT) conference. It was a big buzz all over the popular social media and that morning everyone in our department was talking about it. A miniaturized sequencing device called MinION, which just like a USB flash drive in terms of size and shape, will just put the cost of sequencing to $900. This breakthrough can put genome sequencing right to the doctor’s table within the beginning of next year and revolutionize the way we deliver health-care. But on the other hand, it will further sky-rocket the sequence data volume into an unimaginable height (Blogs on MinION: Pathogens: Genes and Genomes; genomes unzipped). [...]</p> ]]></content:encoded> </item> <item><title>Comment on All genomes are dysfunctional: broken genes in healthy individuals by Links 2/21/12 &#124; Mike the Mad Biologist</title><link>http://www.genomesunzipped.org/2012/02/all-genomes-are-dysfunctional-broken-genes-in-healthy-individuals.php#comment-200835</link> <dc:creator>Links 2/21/12 &#124; Mike the Mad Biologist</dc:creator> <pubDate>Tue, 21 Feb 2012 21:48:05 +0000</pubDate> <guid
isPermaLink="false">http://www.genomesunzipped.org/?p=4369#comment-200835</guid> <description>[...] Link Strengthened By New Study Nasty &#8216;superbug&#8217; is being studied by UB researchers All genomes are dysfunctional: broken genes in healthy individuals It’s a Shark-Eating Shark–Eating–Shark World From depths of the Charles, an ancient [...]</description> <content:encoded><![CDATA[<p>[...] Link Strengthened By New Study Nasty &#8216;superbug&#8217; is being studied by UB researchers All genomes are dysfunctional: broken genes in healthy individuals It’s a Shark-Eating Shark–Eating–Shark World From depths of the Charles, an ancient [...]</p> ]]></content:encoded> </item> <item><title>Comment on Making sequencing simpler with nanopores by So What Could Nanopore Mean for Bacterial Genomics? (And the Pelham 123 Problem) &#124; Mike the Mad Biologist</title><link>http://www.genomesunzipped.org/2012/02/making-sequencing-simpler-with-nanopores.php#comment-200700</link> <dc:creator>So What Could Nanopore Mean for Bacterial Genomics? (And the Pelham 123 Problem) &#124; Mike the Mad Biologist</dc:creator> <pubDate>Tue, 21 Feb 2012 15:05:44 +0000</pubDate> <guid
isPermaLink="false">http://www.genomesunzipped.org/?p=4385#comment-200700</guid> <description>[...] now, you might have heard about Oxford Nanopore&#8216;s first preview of their Gridion and Minion technologies at [...]</description> <content:encoded><![CDATA[<p>[...] now, you might have heard about Oxford Nanopore&#8216;s first preview of their Gridion and Minion technologies at [...]</p> ]]></content:encoded> </item> <item><title>Comment on Making sequencing simpler with nanopores by Oxford Nanopore and the promise of pay-as-you-go sequencing &#124; Eagle Genomics</title><link>http://www.genomesunzipped.org/2012/02/making-sequencing-simpler-with-nanopores.php#comment-200632</link> <dc:creator>Oxford Nanopore and the promise of pay-as-you-go sequencing &#124; Eagle Genomics</dc:creator> <pubDate>Tue, 21 Feb 2012 12:08:50 +0000</pubDate> <guid
isPermaLink="false">http://www.genomesunzipped.org/?p=4385#comment-200632</guid> <description>[...] from &quot;stealth mode&quot; at the AGBT meeting in Florida last week especially so (good coverage here). The technology is appealing as it measures a&#160;single DNA molecule, thus simplifying sample [...]</description> <content:encoded><![CDATA[<p>[...] from &quot;stealth mode&quot; at the AGBT meeting in Florida last week especially so (good coverage here). The technology is appealing as it measures a&nbsp;single DNA molecule, thus simplifying sample [...]</p> ]]></content:encoded> </item> <item><title>Comment on Making sequencing simpler with nanopores by Beyond the Hype &#8211; The Oxford Nano Announcement at AGBT &#171; Omically Speaking</title><link>http://www.genomesunzipped.org/2012/02/making-sequencing-simpler-with-nanopores.php#comment-200180</link> <dc:creator>Beyond the Hype &#8211; The Oxford Nano Announcement at AGBT &#171; Omically Speaking</dc:creator> <pubDate>Mon, 20 Feb 2012 17:59:27 +0000</pubDate> <guid
isPermaLink="false">http://www.genomesunzipped.org/?p=4385#comment-200180</guid> <description>[...]  [...]</description> <content:encoded><![CDATA[<p>[...]  [...]</p> ]]></content:encoded> </item> <item><title>Comment on Making sequencing simpler with nanopores by Genomica hi-tech: Oxford Nanopore presenta il primo sequenziatore usa e getta &#171; my GenomiX</title><link>http://www.genomesunzipped.org/2012/02/making-sequencing-simpler-with-nanopores.php#comment-199942</link> <dc:creator>Genomica hi-tech: Oxford Nanopore presenta il primo sequenziatore usa e getta &#171; my GenomiX</dc:creator> <pubDate>Mon, 20 Feb 2012 07:16:56 +0000</pubDate> <guid
isPermaLink="false">http://www.genomesunzipped.org/?p=4385#comment-199942</guid> <description>[...] parlato d&#8217;altro: ne hanno tessuto le lodi Nature, Forbes, Bio-IT World, New Scientist oltre a diversi blog [...]</description> <content:encoded><![CDATA[<p>[...] parlato d&#8217;altro: ne hanno tessuto le lodi Nature, Forbes, Bio-IT World, New Scientist oltre a diversi blog [...]</p> ]]></content:encoded> </item> </channel> </rss>
