Communication for the Heartland Regional Genetics Group


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"Whitehead, Shona R. (HSC)" <[log in to unmask]>
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Communication for the Heartland Regional Genetics Group <[log in to unmask]>
Thu, 14 Feb 2013 17:14:43 -0600
text/plain (7 kB) , text/html (15 kB) , ACMG-GTR session.pdf (39 kB)

From: Troxell, Robin M.
Sent: Monday, February 11, 2013 9:41 AM
To: Whitehead, Shona R. (HSC)
Subject: FW: Info about Genetests that might be of interest

From: Bocian Maureen
Sent: Sunday, February 10, 2013 7:50 PM
Subject: Important re ACMG conference

Dear Colleagues:

The following is especially important for those of you who plan to attend the ACMG in Phoenix next month, but it has relevance for all of us in clinical genetics and genetic counseling.

As I was looking through the preliminary program, I noticed an ancillary session on Wednesday morning (8-9:30, before the invited sessions begin) entitled:

The NIH Genetic Testing Registry: Public Meeting on Transition Plan with GeneTests.

Wed, 3/20: 8:00 AM - 9:30 AM

Phoenix Convention Center North Building

Room: Ballroom 120 A

The description of the session is attached.  Basically it says that the GeneTests Laboratory Directory will be phased out on June 4, 2013 and that laboratory participation in the GTR is voluntary..... (but, of course, if they get rid of GeneTests there won't be any other option.....).

I encourage all of you who use GeneTests and who consider it too valuable to lose to attend this session so that we can provide input and, if you are so inclined, voice our support for GeneTests as an extremely well-organized, carefully vetted, and highly respected resource.  I worry that if we are not there to stand up for it, we will be left with a much less useful, more confusing entity that is trying to be all things to all people but will end up being too little for too many.

They say that the GTR includes information from GeneReviews and from GeneTests, but when I compared the way genes and disorders are associated in the GTR with the way they are organized on GeneTests, it looks like the GTR has used an entirely different algorithm and classification system, so that when I looked up Marfan under "Genes," I got 3 genes:  FBN1, MED12, and LAMB1.  When I looked up Tuberous Sclerosis, one of the disorders that came up was Focal Cortical Dysplasia of Taylor<https://urldefense.proofpoint.com/v1/url?u=http://www.ncbi.nlm.nih.gov/gtr/tests/334641&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=QD0MALm7li4xmB3DnzvTKy2CVOWeUGJzsljAyiiNZhA%3D%0A&m=EN6HLo7NMbp9bgXtyoYg9s9XdLFyr5%2B6xKHf0YcWb9s%3D%0A&s=ad419661b8ef7ee56cfb9f33954611bdac4a0f0f94db88bafbbb35a0654c8bba>.

When you look up testing for Cystic Fibrosis, you get a list of 167 tests (9 pages of 20 entries each) for 7 conditions in 136 labs-the conditions include CF, absence of the vas deferens, hereditary pancreatitis, inherited lung disorders, bronchiectasis, failure to thrive, and primary ciliary dyskinesia.  The order in which the labs are listed is not clear - not alphabetical, not by type of test, apparently random.  Some entries are just for CFTR, which others have "lung" panels of, e.g. 30-60 different genes.

When I looked up Crouzon, I got 37 tests for 7 conditions in 35 labs - including 5 FGFR2 disorders (Pfeiffer, Beare-Stevenson, Jackson-Weiss, Crouzon, Apert) but also Muenke syndrome and achondroplasia (both FGFR3).  If you then happen to choose achondroplasia from this list, you end up with a single lab that does FGFR3 and lists 8 conditions including Achondroplasia<https://urldefense.proofpoint.com/v1/url?u=http://www.ncbi.nlm.nih.gov/gtr/conditions/C0001080&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=QD0MALm7li4xmB3DnzvTKy2CVOWeUGJzsljAyiiNZhA%3D%0A&m=EN6HLo7NMbp9bgXtyoYg9s9XdLFyr5%2B6xKHf0YcWb9s%3D%0A&s=e4dfee1d6acf32dd9c704b4aa636998b8d67e9888295ec0c6049c6bd4992a466>; Camptodactyly, tall stature, and hearing loss syndrome<https://urldefense.proofpoint.com/v1/url?u=http://www.ncbi.nlm.nih.gov/gtr/conditions/C1864852&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=QD0MALm7li4xmB3DnzvTKy2CVOWeUGJzsljAyiiNZhA%3D%0A&m=EN6HLo7NMbp9bgXtyoYg9s9XdLFyr5%2B6xKHf0YcWb9s%3D%0A&s=75517368ba76a9022fd3f616f6c6abab142de1b2678615b76e2b5e4fb703fe1c>; Crouzon syndrome with acanthosis nigricans<https://urldefense.proofpoint.com/v1/url?u=http://www.ncbi.nlm.nih.gov/gtr/conditions/C2677099&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=QD0MALm7li4xmB3DnzvTKy2CVOWeUGJzsljAyiiNZhA%3D%0A&m=EN6HLo7NMbp9bgXtyoYg9s9XdLFyr5%2B6xKHf0YcWb9s%3D%0A&s=c68cb46a41770ddd6d6b87f414c0b0cf1c794b2e66768477dd7fa067d523e0f5>; Levy-Hollister syndrome<https://urldefense.proofpoint.com/v1/url?u=http://www.ncbi.nlm.nih.gov/gtr/conditions/C0265269&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=QD0MALm7li4xmB3DnzvTKy2CVOWeUGJzsljAyiiNZhA%3D%0A&m=EN6HLo7NMbp9bgXtyoYg9s9XdLFyr5%2B6xKHf0YcWb9s%3D%0A&s=0b99b664c6344f7a52c5f3d4d5432482981b98961ba283b1787d7939b1b92a45>; Muenke syndrome<https://urldefense.proofpoint.com/v1/url?u=http://www.ncbi.nlm.nih.gov/gtr/conditions/C1864436&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=QD0MALm7li4xmB3DnzvTKy2CVOWeUGJzsljAyiiNZhA%3D%0A&m=EN6HLo7NMbp9bgXtyoYg9s9XdLFyr5%2B6xKHf0YcWb9s%3D%0A&s=6d79c3809068b505b86f871d65ed8da674fc4bffd1ca67bb3d285ce1c30d6483>; Thanatophoric dysplasia type 1<https://urldefense.proofpoint.com/v1/url?u=http://www.ncbi.nlm.nih.gov/gtr/conditions/C1868678&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=QD0MALm7li4xmB3DnzvTKy2CVOWeUGJzsljAyiiNZhA%3D%0A&m=EN6HLo7NMbp9bgXtyoYg9s9XdLFyr5%2B6xKHf0YcWb9s%3D%0A&s=0b8be21c2e69ad9f4d60dc86f8899f025967fc0009b886080537ec2354024c61>, Hypochondroplasia<https://urldefense.proofpoint.com/v1/url?u=http://www.ncbi.nlm.nih.gov/gtr/conditions/C0410529&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=QD0MALm7li4xmB3DnzvTKy2CVOWeUGJzsljAyiiNZhA%3D%0A&m=EN6HLo7NMbp9bgXtyoYg9s9XdLFyr5%2B6xKHf0YcWb9s%3D%0A&s=c32f410f94756784c33943ad3e743fb2b14a44db7f2fb93a187d7810e76a0a7b>; and Isolated coronal cynostosis<https://urldefense.proofpoint.com/v1/url?u=http://www.ncbi.nlm.nih.gov/gtr/conditions/CN043619&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=QD0MALm7li4xmB3DnzvTKy2CVOWeUGJzsljAyiiNZhA%3D%0A&m=EN6HLo7NMbp9bgXtyoYg9s9XdLFyr5%2B6xKHf0YcWb9s%3D%0A&s=be4138adfc3c4773b4bb00ef8c5f30a3dd916612fa0d9856eda8fb8d0057f825> (sic).

There are all kinds of filters that can be applied, some of which are useful, but it can quickly get confusing, and it's very difficult to navigate back and forth, to figure out how you got there and how to get back, and to tell whether you have all the information you need at any particular point.  It can't compare with the ease and simplicity of using GeneTests and of teaching with it, as well as the confidence one has in GeneTests' reliability and accuracy.

Please try your best to attend this session - I think it will be very important for all of us.  Please also forward this e-mail to your colleagues in clinical genetics and genetic counseling who plan to attend ACMG.

Thanks - best wishes,


Maureen Bocian, M.D., FAAP, FACMG
Professor of Pediatrics
Division of Genetics and Metabolism
Department of Pediatrics - ZC4482
University of California, Irvine School of Medicine
101 The City Drive
Orange, CA  92868
Tel:  714-456-6873
Fax:  714-456-5330
Pager:  714-506-7087

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