Nabble - Bio.net - Gen-link

Gene translocation

2009-04-29T07:50:49Z

Hi, I saw your post online... I have a trsnslocation of 11 and 22 and have been trying to do online research, also to no avail. I am 23. As your post was 
listed 10 years ago I'm guessing this address won't work any more, but I'd really like to communicate with someone else with a translocation, as there seems to be no
support group and it can feel so lonely. If you knew of any useful addresses/groups/etc I would really appreciate it.

Kitty Ballard


"I was recently told that I have a gene translocation of 15 and 22.  I have been
trying to do some research on the internet with no luck.  Can someone help me
with some information?  I want to know about my chances of having healthy
children and what is involved.  I am a thirty year old female.  Thanks, Katie"

http://www.bio.net/bionet/mm/gen-link/1999-January/001589.html

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Re: Gen-link Digest, Vol 20, Issue 1

2008-12-21T21:06:38Z

hi, instead use easylinkage from sourceforge(ggogle it) .you can
install it to c:programme files and then click on the exe.file and
follow instructions on the screen.
Kiran

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> Date: Sat, 20 Dec 2008 03:36:11 -0600
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> Can anyone guide me to download mapmaker exp files to windows vista
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(no subject)

2008-12-20T01:36:11Z

Hai

Can anyone guide me to download mapmaker exp files to windows vista operating system.

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Re: Gen-link Digest, Vol 19, Issue 2

2008-06-13T09:25:03Z

pls use easylinkage package its simple and non complicated,,, http://sourceforge.net/projects/easylinkage/
easy trouble shooting..
kiran

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Today's Topics:

1. problem wtith mlink (ohouyem@...)

----------------------------------------------------------------------

Message: 1
Date: Tue, 10 Jun 2008 11:40:40 -0700 (PDT)
From: ohouyem@...
Subject: [Genetic-linkage] problem wtith mlink
To: bionet-molbio-gene-linkage@...
Cc: o_houyem@...
Message-ID:
<2d21f1f6-9dc9-496d-b4fb-3807116a1ad9@...>
Content-Type: text/plain; charset=windows-1252

Hi professionals!

I have a problem with mlink. I want to evaluate the risk of a fetus to
be affected. I have his genotype with three markers flanking the
morbid gene. The disease is autosomal recessive, with incomplete
penetrance.

I used mlink for this purpose, but I have this error message:
"Fatal error detected in procedure inputdata
Error detected reading pedigree record 1. Illegal code for sex 17"

I indicate the sex of the fetus, and the affected allele as
undetermined. Bur I have the same error message.

Please please , I'm waiting for your help
Thank you

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End of Gen-link Digest, Vol 19, Issue 2
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regards,
kiran
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problem wtith mlink

2008-06-10T11:40:40Z

Hi professionals!

I have a problem with mlink. I want to evaluate the risk of a fetus to
be affected. I have his genotype with three markers flanking the
morbid gene. The disease is autosomal recessive, with incomplete
penetrance.

I used mlink for this purpose, but I have this error message:
“Fatal error detected in procedure inputdata
Error detected reading pedigree record 1. Illegal code for sex 17”

I indicate the sex of the fetus, and the affected allele as
undetermined. Bur I have the same error message.

Please please , I’m waiting for your help
Thank you

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JoinMap & MapQTL software

2008-06-02T07:39:59Z

Hello. I used this software as a graduate student for QTL mapping in cichlid
fish and would now like to purchase them for my lab. Could you please send
ordering information? Thank you very much.

Best regards,
Craig

--------------------
R. Craig Albertson, Ph.D.
Assistant Professor
Department of Biology
Syracuse University
130 College Place
Syracuse, NY 13244
Office: 315-443-8106; Lab: 315-443-8193
Fax: 315-443-2012
rcalbert@...

http://biology.syr.edu/albertson

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SAS and cluster analysis

2008-01-30T13:23:05Z

SAS and cluster analysis

Hi! Mickey,

I saw your posted question as follows. Have you every gotten

A response and did you solve the missing cell issue in using Proc cluster.

I am facing the same issue now. Can you share your idea about this.

Thanks

Yuefu Liu

St Louis

------------------------------------------------------

well, here's my second post in regards to cluster analysis. the question

is the same as last time except now i'm using SAS: has anyone ever used

SAS for cluster analysis and how did you account for missing values from

the data martix (in qualitative anlyses) without the program simply

rejecting the sample?

thanks in advance,

mick

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remeinder ICAPSS2008

2007-12-13T04:32:41Z

Dear all;

This is a gentle reminder that the DEADLINE for registration for the 2008 ICAPSS in Conference is April 8, 2008, Samsun, Turkey.

Now, social programs and other facilities are available in our web pages. Meeting registration link www.icapss.com/registration.asp. Abstracts are due Jan 15, 2008.

Please free to contact us if you have any questions regarding the ICAPSS and the upcoming workshop and courses. please visit our website: www.icapss.com More details will follow in January.

Serhat

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genomic isolation for Acetobacter xylinum

2007-11-16T15:43:16Z

Hello,

I have some kind of problem. I need quickly method for genomic isolation DNA from Acetobacter xylinum and I wonder which commercial kit would be the greatest? Could You help me? Does anyone do isolation from this bacteria?

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Linkage using 240S Illumina chips

2007-08-24T15:53:22Z

I was looking for help on how to use data from 240S Illumina chips for linkage. I ran a family on these chips which genotype 240,000 SNPs across the genome. Unfortunately none of the linkage programs that I have looked at are able to handle this amount of data. Even SNPlink which is designed to cut down the large numbers of SNPs does not work with such a large dataset. One approach that I was thinking of following is to match the SNPs on Illumina’s linkage panel V to the SNPs that I have generated using the 240S SNP chip. Problem is that not all of the linkage panel V SNPs are on the 240S Illumina SNP chip, so I may have to take nearby SNPs. My questions are as follows:

(1) Has anyone any experience with using 240S or 550K Illumina SNP chips for linkage studies?

(2) Does anyone have a list of SNPs on the 240S SNP chip that they know work for linkage?

Many thanks in advance,

Best,

Bryan

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Primer Design for Microsatellites

2007-07-25T14:00:21Z

Hi,
Thanks for all the replies to the previous posting, guys. I have now
ordered the primers, and have a commercial sequencing question. I plan to
fluorescently tag the primers when I verify that they work, and am looking
to send the resulting tagged PCR products to a company that can do an
AFLP/microsatellite variability assay on them, since we don't have an
automated sequencer and I would like to avoid manually running and
analyzing sequencing gels. What companies can provide that service for a
reasonable price? Also, if I do end up doing it myself, any ideas on how
to simplify the procedure overall? Anything radioactive is out of the
question, but I have read others doing silver staining with polyacrilamide
gels rather than flourescent tagging, and even running agarose gels.
Thanks.

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Primer Design for Microsatellites

2007-07-16T12:56:30Z

Hi,
I'm in the process of developing microsatellite primers to study box
turtle hybridization, and I am now at the initial stage of actual primer
design. Any recommendations as to what software is best for designing
primers for microsats? I'm currently exploring Invitrogen's Vector NTI and
B. Fairthcloth's Msatcommander (works off of primer 3.) Also, any advice
on what is the best way to process and analyze samples once the microsat
regions are ID'd and primers are designed? I'm going to need to do a few
hundred samples, and our facilities do not have a functional sequencer.
What companies out there do cheap AFLP analysis? Thanks.

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questions for analysis QTL using QTL cartographer

2007-04-29T14:46:45Z

Hi All,
I am using QTL Cartographer to analysis some datasets. I got 3 datasets from my boss, one is the mapmaker file 'truemap.maps' and the others are the original raw files, 'allmarkers.raw' and 'subsetmarkers.raw'. They are the same datasets and only difference is the former one contain all the genetic markers which are constant as the 'truemap.maps' and the later one only have the have markers.

Boss requested me to use the map file she gave me (i.e., translate using QTL-Cartographer), and analyze both datasets. Thus, I am wondering is that possible for me using the map file to analyze the 'subsetmarker.raw' without use Emap to make a new map file. If possible, what should I do?
Thanks a lot!
Charles

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RE: BRCA1, BRCA2 CLIA Reference Lab Seeks Medical Affairs Director

2007-04-01T10:05:57Z

Message

Hi Ann Marie,

You may try Steven Narod’s Lab in Toronto, Canada, for BRCA1 and BRCA2 testing. You could also try Jacques Simard in Quebec, Canada.

From: gen-link-bounces@... [mailto:gen-link-bounces@...] On Behalf Of Ronders, Ann Marie
Sent: Thursday, March 29, 2007 4:37 PM
To: gen-link@...
Subject: [Genetic-linkage] BRCA1,BRCA2 CLIA Reference Lab Seeks Medical Affairs Director

I am looking for a lab to possibly contract with for BRAC testing. Please advise if interested.

Ann Marie Ronders, RN, MA, CCM

U M Manager of Clinical Services

Greater Newport Physicians

Hoag Hospital

Phone 949 764-1430

Fax 949 764-6982

annmarie.ronders@...annmarie.ronders@...org

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Thank you,

Hoag Memorial Hospital Presbyterian and its Affiliates

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BRCA1, BRCA2 CLIA Reference Lab Seeks Medical Affairs Director

2007-03-29T14:36:31Z

Message

I am looking for a lab to possibly contract with for BRAC testing. Please advise if interested.

Ann Marie Ronders, RN, MA, CCM

U M Manager of Clinical Services

Greater Newport Physicians

Hoag Hospital

Phone 949 764-1430

Fax 949 764-6982

annmarie.ronders@...org

Thank you,

Hoag Memorial Hospital Presbyterian and its Affiliates

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Chi square test

2007-03-12T09:26:58Z

Hello Friends,
I am trying to assess the segregation of a transcript which i transformed to arabidopsis.
I have T2 and T3 generation seeds and i have selected them on Kanamycin and got Kan+ and Kan- plants.
my problem is 'How to do Chi square Test' by correlating my selection data?
can anybody teach me how to do the Chi square test?

thank you in advance

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SUMMER TRAINING @ DNA RESEARCH CENTRE

2007-03-05T22:18:57Z

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The deluge of data shows no sign of abating, particularly as new
technologies appear (protein chips) and established technologies are
improved (mass spectrometers, DNA micro-arrays) or re-implemented on
industrial scales. Finding new ways to integrate, manage, visualize,
and interpret data from diverse sources is one of the grand challenges
for modern bioinformatics, which merges information technology,
computer science, statistics, applied mathematics, and biology. Topics
of interest to this workshop include, but are not limited to:

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mRNA and protein _expression

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Phone : +91- 40 - 40180502
Mobile : +91 - 0 - 9247438983
e-Mail : dnaresearchcentre@...
Visit us at: www.dnares.in

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regarding calculation

2007-01-06T21:41:30Z

Gene distances calculation /recombination percentage calculation for characters each showing complementary gene action(9:7).For 9:7/9:7combination formulae were not derived by Allard.Can anyone help in the derivation of the formula.

c_varalakshmi@...

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Free software for linkage analysis in large pedigrees

2006-12-14T13:11:53Z

Dear Claus:

Where can I download your program "Block"?

Thank you very much,

Jinying Zhao, MD, PhD
Emory University

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microsatellites

2006-11-17T01:52:22Z

dear all,

im trying to do association studies with microsatellites, which are present in a disease locus. im planning to order for about 10 microsatellites in this region. i got six markers from ncbi site, if want want more to fill in the gaps, where can i find the information for that other than ncbi ? and what should be the optimium spacing for the markers ?

kindly advice me.

linda koshy

Mrs.Linda Koshy
Human Molecular Genetics Lab
Rajiv Gandhi Centre For Biotechnology
Poojapura, Thycaud po
Trivandrum-695014 Kerala. India.
Tel: 91-471-2341716, 2347975
Mob: 9447058394

Fax: +91 0471-2348096

email: lindakoshy@...

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POINTER DOS or MAC VER

2006-09-12T19:28:03Z

Greetings all. We are doing some inheritance analyses and found that
pointer could help, does anybody could point us out where be could
download a DOS compiled ver or a MAC ver different from the SUN verfound
in the FTP, could somebody provide me a with a copy of the executable and
documentation?

Thanks in advance,
John Castiblanco

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help needed in breaking loops

2006-07-18T16:46:36Z

Hi Dr. Schaeffer,
I am a graduate student at NCSU. I have a pedigree data of dogs which
contains many loops (may be 200). I am using FASTLINK software to find
the recombination rates between markers. I can use MAKEPED to break the
loops but I have to assign the loops manually in MAKEPED. Can you
please let me know if the newer version of FASTLINK can detect and break
the loops automatically ?

Thanks in advance,

Regards
Suvajit Samanta

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Homozygosity analysis

2006-06-01T11:44:17Z

Hi,
Recently i was searching on net about programs for analyzing
homozygosity analysis using 10Karrays and with only affected
individuals. I found a program for 4members in a family/2members and
even for only affected individuals. Then i did not save the search
result, now iam unable to retrieve. Does anyone know about the
program?pls help me -Ram

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Re: Quick Genetics problem help

2006-05-01T23:28:14Z

The magnitude of the lod score and where it is high vs. low depends on a
number of factors:
1) Heterogeneity. There can be genetic heterogeneity, and even slight
nuances in how a sample was obtained can affect ones ability to detect
linkage at one site vs. another. Differences in the phenotype used to
collect the sample would be one indicator of possible heterogeneity.
2) The "Suarez" effect. When there is heterogeneity, replication of a
result often requires a larger sample size than the initial finding,
because the initial report is the best of several possiblities, while
replication requires a strong score in the same location. Are there any
hints of positive lod scores at the second site across studies?
3) Bad luck or other "problems" with the analysis. One or both could be
wrong. There are lots of ways one can end up with false positive results,
some of which result from bad (naive) applications of the analysis
methods, and some of which simply reflect badk luck.

************************************************************************
Ellen M. Wijsman COURIER DELIVERY ADDRESS ONLY:
Research Professor Ellen M. Wijsman
Div. of Medical Genetics and 1914 N 34th St., suite 209
Dept. Biostatistics Seattle, WA 98103
BOX 357720, University of Washington (Note: Use this address
Seattle, WA 98195-7720 EXACTLY as given above, and
phone: (206) 543-8987 use ONLY for courier delivery!!!)
fax: (206) 616-1973 email: wijsman@...
web page: http://faculty.washington.edu/wijsman
*************************************************************************

On Mon, 1 May 2006, Dembsky, Joshua Lyman (UMKC-Student) wrote:

> Hello all!
>
> I am a graduate student in Kansas City. I have having some problems understanding a basic genetics concept that I am hoping one of you can help me with.
>
> If you have two chromosomes each with an area that has been identified as an area of linkage for a particular trait, what are some of the reasons you can have different lod scores? For example, if two academic groups have identified an area of linkage of a trait, one study found an area on chromosome 7 with a lod score of 6.00 and another study found an area on chromosome 13 with a lod score of 5.20, how do you explain the different linkage results?
>
> Your assistance is greatly appreciated!
> jldxt9@...
> Josh Dembsky
> University of Missouri-Kansas City
>
>

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Quick Genetics problem help

2006-05-01T05:40:45Z

Hello all!

I am a graduate student in Kansas City. I have having some problems understanding a basic genetics concept that I am hoping one of you can help me with.

If you have two chromosomes each with an area that has been identified as an area of linkage for a particular trait, what are some of the reasons you can have different lod scores? For example, if two academic groups have identified an area of linkage of a trait, one study found an area on chromosome 7 with a lod score of 6.00 and another study found an area on chromosome 13 with a lod score of 5.20, how do you explain the different linkage results?

Your assistance is greatly appreciated!
jldxt9@...
Josh Dembsky
University of Missouri-Kansas City

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FASTLINK for DOS available

2006-04-12T09:09:46Z

Hello Alex Schaffer,

I use the fastlink package on a PC and it runs fine. Nevertheless, I work
with cattle pedigrees with much many matings / bull.
In the unknown program I use is limited to 3 matings / one male.
Since I am not really familiar with compiling these programs - is it
possible to get a version workin with larger families (e.g. 30 matings /
male and 10 matings / female).

Thank you in advance,

Johannes Buitkamp

- - - - - - - - - - - - - - - - -
Besuchen Sie uns am Sonntag, den
02. Juli 2006 bei unserem Tag der
offenen Tür in Freising-Weihenstephan
Mehr Informationen unter http://www.LfL.bayern.de

_________________________________________ITZ
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Institut f Tierzucht
Bayerische Landesanstalt fuer Landwirtschaft
Prof.-Duerrwaechter-Platz 1
85580 Grub/Germany

phone: +49-89-99 141 130
fax: +49-89-99 141 199
e-Mail: Johannes.Buitkamp@...
WEB: http://www.lfl.bayern.de
_________________________________________LfL

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MCF7 and MDA MB 231 polymorphisms

2006-03-07T10:33:25Z

I need to find some polymorphisms and/or mutations in the tumor cell lines MCF7 and MDA MB 231.

SNPs and small mutations are preferred.

Could anyone suggest a way or directly tell some of these polymorphisms?

Thanks,

Emre

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