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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>Tue, 21 May 2013 22:42:30 +0000</lastBuildDate> <sy:updatePeriod>hourly</sy:updatePeriod> <sy:updateFrequency>1</sy:updateFrequency> <generator>http://wordpress.org/?v=3.5.1</generator> <item><title>Comment on Cluster Sequencing with Oxford Nanopore&#8217;s GridION System by Nanopore Sequencing by Divine Intervention? - Homologus</title><link>http://www.genomesunzipped.org/2011/01/cluster-sequencing-with-oxford-nanopores-gridion-system.php#comment-1006061</link> <dc:creator>Nanopore Sequencing by Divine Intervention? - Homologus</dc:creator> <pubDate>Tue, 21 May 2013 22:42:30 +0000</pubDate> <guid
isPermaLink="false">http://www.genomesunzipped.org/?p=2547#comment-1006061</guid> <description><![CDATA[[...] Jan 2011: Cluster Sequencing with Oxford Nanopore’s GridION System [...]]]></description> <content:encoded><![CDATA[<p>[...] Jan 2011: Cluster Sequencing with Oxford Nanopore’s GridION System [...]</p> ]]></content:encoded> </item> <item><title>Comment on Ten guidelines for tweeting at conferences by shortterm loans</title><link>http://www.genomesunzipped.org/2012/11/ten-guidelines-for-tweeting-at-conferences.php#comment-1005763</link> <dc:creator>shortterm loans</dc:creator> <pubDate>Tue, 21 May 2013 20:15:23 +0000</pubDate> <guid
isPermaLink="false">http://www.genomesunzipped.org/?p=5233#comment-1005763</guid> <description><![CDATA[lpajvfdjt ezvnqgxevpl jwwmwwhr ibtkaew rhonrjqzhq qbcsxioh aawnppqy]]></description> <content:encoded><![CDATA[<p>lpajvfdjt ezvnqgxevpl jwwmwwhr ibtkaew rhonrjqzhq qbcsxioh aawnppqy</p> ]]></content:encoded> </item> <item><title>Comment on Identification of genomic regions shared between distant relatives by Greg Magoon</title><link>http://www.genomesunzipped.org/2013/05/identification-of-genomic-regions-shared-between-distant-relatives.php#comment-993837</link> <dc:creator>Greg Magoon</dc:creator> <pubDate>Mon, 20 May 2013 01:44:59 +0000</pubDate> <guid
isPermaLink="false">http://www.genomesunzipped.org/?p=5518#comment-993837</guid> <description><![CDATA[If you are considering blocks of say 10 Mb or larger being tens of generations old, then WGS could help provide a rough indication of their age, at least in an aggregate/average sense. Given a germline mutation rate of about 1E-8/site/generation (http://www.sciencemag.org/content/328/5978/636.short), this would suggest an average of 1 mutation in the shared segment for every 5 generations back (i.e. 5 generations on each side for a total of 10 generations) for a 10 Mb block. If aggregated over a sufficient number of shared segments to account for mutation rate variability (http://www.nature.com/ng/journal/v43/n7/full/ng.862.html), stochastic effects, etc., this could be an interesting empirical test of your hypotheses.]]></description> <content:encoded><![CDATA[<p>If you are considering blocks of say 10 Mb or larger being tens of generations old, then WGS could help provide a rough indication of their age, at least in an aggregate/average sense. Given a germline mutation rate of about 1E-8/site/generation (<a
href="http://www.sciencemag.org/content/328/5978/636.short" rel="nofollow">http://www.sciencemag.org/content/328/5978/636.short</a>), this would suggest an average of 1 mutation in the shared segment for every 5 generations back (i.e. 5 generations on each side for a total of 10 generations) for a 10 Mb block. If aggregated over a sufficient number of shared segments to account for mutation rate variability (<a
href="http://www.nature.com/ng/journal/v43/n7/full/ng.862.html" rel="nofollow">http://www.nature.com/ng/journal/v43/n7/full/ng.862.html</a>), stochastic effects, etc., this could be an interesting empirical test of your hypotheses.</p> ]]></content:encoded> </item> <item><title>Comment on Inbreeding, Genetic Disease and the Royal Wedding by Dora Smith</title><link>http://www.genomesunzipped.org/2011/04/inbreeding-genetic-disease-and-the-royal-wedding.php#comment-991455</link> <dc:creator>Dora Smith</dc:creator> <pubDate>Sun, 19 May 2013 16:45:01 +0000</pubDate> <guid
isPermaLink="false">http://www.genomesunzipped.org/?p=3210#comment-991455</guid> <description><![CDATA[Something else I forgot to mention.  VERY important.  Minus exacerbating factors, like a steady diet of red wine laced with lead, walls lined with lead paint, etc., children who were never washed, severe inbreeding in a family that carries the gene, etc., etc., genetic metabolic porphyria is absolutely silent in 90% of people who have it.  Blood work usually reveals a characteristic deficiency of the affected enzyme, but the heme biosynthetic pathway has considerable excess capacity in normal healthy people who don&#039;t have heavy metal poisoning and whatever.  Most of the people who DO get acute attacks of porphyria, other things being normal, have a difference in the way they metabolize certain kinds of hormones that the body normally makes, which is shaped around the time people are born.
However.  Most people with genetic metabolic porphyria have characteristic defects that show up on certain brain scans, like holes in the basal ganglia, and are characteristically intense and nervous - similar to someone with a bipolar temperament.
During the dark ages, the other word for bipolar disorder was feudal warlord temperament.  Most warlords came to power by being ambitious and obsessive and mad enough to frighten people.  Those whose families held power didn&#039;t for instance suffer repeated attacks of madness like someone with severe bipolar disorder.  One tends to suspect that genetic metabolic porphyria selected itself into the royal lines.  Most royal lineages lived simply, in ways that would not have aggravated porphyria into acute attacks, during their first several generations.  Morover, repeated bouts of illess that resembled George VI&#039;s were characteristic of, for example the kings of Wessex, and they just lived with them.   The Merovingian kings had repeated attacks of madness, sometimes accompanied by peripheral paralysis.   These high aristocratic lines fed into each other, even when the connections can&#039;t be traced.]]></description> <content:encoded><![CDATA[<p>Something else I forgot to mention.  VERY important.  Minus exacerbating factors, like a steady diet of red wine laced with lead, walls lined with lead paint, etc., children who were never washed, severe inbreeding in a family that carries the gene, etc., etc., genetic metabolic porphyria is absolutely silent in 90% of people who have it.  Blood work usually reveals a characteristic deficiency of the affected enzyme, but the heme biosynthetic pathway has considerable excess capacity in normal healthy people who don&#8217;t have heavy metal poisoning and whatever.  Most of the people who DO get acute attacks of porphyria, other things being normal, have a difference in the way they metabolize certain kinds of hormones that the body normally makes, which is shaped around the time people are born.</p><p>However.  Most people with genetic metabolic porphyria have characteristic defects that show up on certain brain scans, like holes in the basal ganglia, and are characteristically intense and nervous &#8211; similar to someone with a bipolar temperament.</p><p>During the dark ages, the other word for bipolar disorder was feudal warlord temperament.  Most warlords came to power by being ambitious and obsessive and mad enough to frighten people.  Those whose families held power didn&#8217;t for instance suffer repeated attacks of madness like someone with severe bipolar disorder.  One tends to suspect that genetic metabolic porphyria selected itself into the royal lines.  Most royal lineages lived simply, in ways that would not have aggravated porphyria into acute attacks, during their first several generations.  Morover, repeated bouts of illess that resembled George VI&#8217;s were characteristic of, for example the kings of Wessex, and they just lived with them.   The Merovingian kings had repeated attacks of madness, sometimes accompanied by peripheral paralysis.   These high aristocratic lines fed into each other, even when the connections can&#8217;t be traced.</p> ]]></content:encoded> </item> <item><title>Comment on Inbreeding, Genetic Disease and the Royal Wedding by Dora Smith</title><link>http://www.genomesunzipped.org/2011/04/inbreeding-genetic-disease-and-the-royal-wedding.php#comment-991397</link> <dc:creator>Dora Smith</dc:creator> <pubDate>Sun, 19 May 2013 16:29:15 +0000</pubDate> <guid
isPermaLink="false">http://www.genomesunzipped.org/?p=3210#comment-991397</guid> <description><![CDATA[One other thing.  George VI had a fifth brother, who was sickly and neurologically damaged, and kept having seizures, and only lived to be 15.   He was eventually isolated in a house at Sandringham because the king and queen didn&#039;t want people to be aware of him.  I think he was eventually buried there.]]></description> <content:encoded><![CDATA[<p>One other thing.  George VI had a fifth brother, who was sickly and neurologically damaged, and kept having seizures, and only lived to be 15.   He was eventually isolated in a house at Sandringham because the king and queen didn&#8217;t want people to be aware of him.  I think he was eventually buried there.</p> ]]></content:encoded> </item> <item><title>Comment on Inbreeding, Genetic Disease and the Royal Wedding by Dora Smith</title><link>http://www.genomesunzipped.org/2011/04/inbreeding-genetic-disease-and-the-royal-wedding.php#comment-991382</link> <dc:creator>Dora Smith</dc:creator> <pubDate>Sun, 19 May 2013 16:25:12 +0000</pubDate> <guid
isPermaLink="false">http://www.genomesunzipped.org/?p=3210#comment-991382</guid> <description><![CDATA[One other thing; children born with two bad copies of the genes for protoporphyrinogen oxidase and coproporphyrinogen oxidase make very little of the affected enzyme of the heme biosynthetic pathway (the heme from which is used for metabolic enzymes; hemoglobin is made by its own genes).   They are characteristically very sickly and undersized, often neurologically damaged, and they very often don&#039;t live very long.  Since porphyria has been traced in the royal lines to the Spanish, French, English and Habsurg lines in the 15th century, and these lines were extremely inbred, they were having alot of children with homozygous porphyria, and that fact explains much.  I think that Henry VIII and Catherine of Aragon actually had fifteen children, certainly a large number of them, including several sons, but only Mary survived.   William of Orange was badly stunted in growth and had severe neurological damage, probably to his respiratory nerves among other things.  He was raised in a simple Protestant household; kept very clean and fed simple food and no alcohol, and his doctors tended to avoid medicine; that enabled him to survive.]]></description> <content:encoded><![CDATA[<p>One other thing; children born with two bad copies of the genes for protoporphyrinogen oxidase and coproporphyrinogen oxidase make very little of the affected enzyme of the heme biosynthetic pathway (the heme from which is used for metabolic enzymes; hemoglobin is made by its own genes).   They are characteristically very sickly and undersized, often neurologically damaged, and they very often don&#8217;t live very long.  Since porphyria has been traced in the royal lines to the Spanish, French, English and Habsurg lines in the 15th century, and these lines were extremely inbred, they were having alot of children with homozygous porphyria, and that fact explains much.  I think that Henry VIII and Catherine of Aragon actually had fifteen children, certainly a large number of them, including several sons, but only Mary survived.   William of Orange was badly stunted in growth and had severe neurological damage, probably to his respiratory nerves among other things.  He was raised in a simple Protestant household; kept very clean and fed simple food and no alcohol, and his doctors tended to avoid medicine; that enabled him to survive.</p> ]]></content:encoded> </item> <item><title>Comment on Inbreeding, Genetic Disease and the Royal Wedding by Dora Smith</title><link>http://www.genomesunzipped.org/2011/04/inbreeding-genetic-disease-and-the-royal-wedding.php#comment-991339</link> <dc:creator>Dora Smith</dc:creator> <pubDate>Sun, 19 May 2013 16:16:00 +0000</pubDate> <guid
isPermaLink="false">http://www.genomesunzipped.org/?p=3210#comment-991339</guid> <description><![CDATA[The book that revealed that George VI&#039;s brother was diagnosed with porphyria, showed that the tests failed to adequately distinguish which form of metabolic porphyria he had.   Variegate porphyria and hereditary coproporphyria look very similar on the tests for levels of assorted porphyrins that were done.   What needed to be done was specific assays for two different enzymes; protoporphyrinogen oxidase and coproporphyrinogen oxidase, to determine which was present at only half its normal level (because of having one nonfunctioning copy of the gene).  This was not done.  The same author sequenced most but not all of the gene for protoporphyrinogen oxidase in somebody he expected to have the royal porphyria, and did not find it.   The gene for coproporphyrinogen oxidase was never searched.
Hereditary coproporphyria is characateristically milder than variegate porphyria, so would more often be expected to be silent or mild and vague.  It is well recognized that through George VI&#039;s generation, royalty did things that aggravated porphyria, from heavy metals in the paint to same in their wine to same in their medicines.  People with metabolic porphyria actually can&#039;t take many drugs because heme enzymes are needed to metabolize them, and some block the production of these enzymes.   The royal family themselves believed that whatever ailed George VI and his brothers was caused by starvation, dosing with alcohol, and poor cleanliness, all parts of abusive care by their nurse, and all of that would have aggravated genetic metabolic porphyria.
George VI&#039;s repeated attacks of acute digestive symptoms and extreme nervousness were far more characteristic of a typical attack of porphyria than George III&#039;s more severe attacks, that probably were aggravated by his medical care.   One time he escaped, went to the seashore, ate porridge, and got well, which pretty much is the strategy that used to work on one of these genetic mutations that has become common in a part of Scandinavia.   When these people started going to hospitals they started getting much sicker and dying.   Evidently, by the time George VI was in the navy, the royal doctors had absorbed the information that whatever else you do, you do NOT give this family medicine.  They kept prescribing rest and milk toast.  His attacks were likely caused by conditions on board naval vessels.  At the same time as they removed his appendix, he withdrew from the navy, and I guess he never had another acute attack, though his nerves and bad temper were the stuff of legend.
Dora]]></description> <content:encoded><![CDATA[<p>The book that revealed that George VI&#8217;s brother was diagnosed with porphyria, showed that the tests failed to adequately distinguish which form of metabolic porphyria he had.   Variegate porphyria and hereditary coproporphyria look very similar on the tests for levels of assorted porphyrins that were done.   What needed to be done was specific assays for two different enzymes; protoporphyrinogen oxidase and coproporphyrinogen oxidase, to determine which was present at only half its normal level (because of having one nonfunctioning copy of the gene).  This was not done.  The same author sequenced most but not all of the gene for protoporphyrinogen oxidase in somebody he expected to have the royal porphyria, and did not find it.   The gene for coproporphyrinogen oxidase was never searched.</p><p>Hereditary coproporphyria is characateristically milder than variegate porphyria, so would more often be expected to be silent or mild and vague.  It is well recognized that through George VI&#8217;s generation, royalty did things that aggravated porphyria, from heavy metals in the paint to same in their wine to same in their medicines.  People with metabolic porphyria actually can&#8217;t take many drugs because heme enzymes are needed to metabolize them, and some block the production of these enzymes.   The royal family themselves believed that whatever ailed George VI and his brothers was caused by starvation, dosing with alcohol, and poor cleanliness, all parts of abusive care by their nurse, and all of that would have aggravated genetic metabolic porphyria.</p><p>George VI&#8217;s repeated attacks of acute digestive symptoms and extreme nervousness were far more characteristic of a typical attack of porphyria than George III&#8217;s more severe attacks, that probably were aggravated by his medical care.   One time he escaped, went to the seashore, ate porridge, and got well, which pretty much is the strategy that used to work on one of these genetic mutations that has become common in a part of Scandinavia.   When these people started going to hospitals they started getting much sicker and dying.   Evidently, by the time George VI was in the navy, the royal doctors had absorbed the information that whatever else you do, you do NOT give this family medicine.  They kept prescribing rest and milk toast.  His attacks were likely caused by conditions on board naval vessels.  At the same time as they removed his appendix, he withdrew from the navy, and I guess he never had another acute attack, though his nerves and bad temper were the stuff of legend.</p><p>Dora</p> ]]></content:encoded> </item> <item><title>Comment on Making sequencing simpler with nanopores by Nanopore Sequencing by Divine Intervention? - Homologus</title><link>http://www.genomesunzipped.org/2012/02/making-sequencing-simpler-with-nanopores.php#comment-966962</link> <dc:creator>Nanopore Sequencing by Divine Intervention? - Homologus</dc:creator> <pubDate>Thu, 16 May 2013 19:52:38 +0000</pubDate> <guid
isPermaLink="false">http://www.genomesunzipped.org/?p=4385#comment-966962</guid> <description><![CDATA[[...] Feb 2012: Making sequencing simpler with nanopores [...]]]></description> <content:encoded><![CDATA[<p>[...] Feb 2012: Making sequencing simpler with nanopores [...]</p> ]]></content:encoded> </item> <item><title>Comment on ACMG guidelines on IFs – responding to the response… by Matt Thomas</title><link>http://www.genomesunzipped.org/2013/05/acmg-guidelines-on-ifs-responding-to-the-response.php#comment-966776</link> <dc:creator>Matt Thomas</dc:creator> <pubDate>Thu, 16 May 2013 19:21:48 +0000</pubDate> <guid
isPermaLink="false">http://www.genomesunzipped.org/?p=5514#comment-966776</guid> <description><![CDATA[&quot;The clarification attempts to affirm both these positions by saying that opportunistic screening of children for adult onset conditions they probably don’t have is fine, but diagnostic testing for conditions they are at high risk for is not. That logic doesn’t make any sense&quot;
ACMG&#039;s logic does make sense if you prioritize the prevention of disease for at-risk family members.
Before next-gen sequencing, the way a clinician would know a healthy child was at risk for a medically actionable, adult-onset condition would be if someone else in the family was diagnosed with it. In this situation, there is already an opportunity for all the older at-risk relatives to be warned and the child&#039;s testing can be deferred until s/he is an adult and/or clinical screening begins.
After next-gen sequencing, a child&#039;s incidental finding may inform family members of their risk for a serious disease amenable to screening/treatment before anyone in the family has become sick. It seems preferable to incidentally detect a hereditary disease in a family through a child&#039;s exome sequencing versus after a family member develops an illness that could have been prevented or detected at a stage more responsive to treatment.]]></description> <content:encoded><![CDATA[<p>&#8220;The clarification attempts to affirm both these positions by saying that opportunistic screening of children for adult onset conditions they probably don’t have is fine, but diagnostic testing for conditions they are at high risk for is not. That logic doesn’t make any sense&#8221;</p><p>ACMG&#8217;s logic does make sense if you prioritize the prevention of disease for at-risk family members.</p><p>Before next-gen sequencing, the way a clinician would know a healthy child was at risk for a medically actionable, adult-onset condition would be if someone else in the family was diagnosed with it. In this situation, there is already an opportunity for all the older at-risk relatives to be warned and the child&#8217;s testing can be deferred until s/he is an adult and/or clinical screening begins.</p><p>After next-gen sequencing, a child&#8217;s incidental finding may inform family members of their risk for a serious disease amenable to screening/treatment before anyone in the family has become sick. It seems preferable to incidentally detect a hereditary disease in a family through a child&#8217;s exome sequencing versus after a family member develops an illness that could have been prevented or detected at a stage more responsive to treatment.</p> ]]></content:encoded> </item> <item><title>Comment on Identification of genomic regions shared between distant relatives by Graham</title><link>http://www.genomesunzipped.org/2013/05/identification-of-genomic-regions-shared-between-distant-relatives.php#comment-950357</link> <dc:creator>Graham</dc:creator> <pubDate>Tue, 14 May 2013 22:39:13 +0000</pubDate> <guid
isPermaLink="false">http://www.genomesunzipped.org/?p=5518#comment-950357</guid> <description><![CDATA[Emanuel: Note that NGS alone will not offer a huge improvement of identifying distant relatives (say &lt;10 generations ago), as the the limiting factor here is that the long shared identical blocks are highly variable in length. Having full sequence won&#039;t side step that problem, we will still have large uncertainty about when these shared blocks come from.]]></description> <content:encoded><![CDATA[<p>Emanuel: Note that NGS alone will not offer a huge improvement of identifying distant relatives (say &lt;10 generations ago), as the the limiting factor here is that the long shared identical blocks are highly variable in length. Having full sequence won&#039;t side step that problem, we will still have large uncertainty about when these shared blocks come from.</p> ]]></content:encoded> </item> </channel> </rss>