Genotyping & Linkage Analysis WWW links

• The deCODE genetic map is available as "Web Table E" in the Supplemental Data for Kong et al, Nature Genetics 31, 241-247 (2002) (PMID: 12053178)
• An annotated slideshow of mine, entitled Mapping human disease genes with Affymetrix 10K SNP chips and the HMS Orchestra Shared Research Cluster. We are using Orchestra to calculate 10,000 multipoint lod scores with Linkmap or Vitesse.
• A short explanation of linkage analysis, from the Engle lab at Children's Hospital, Boston.
• Alejandro Schäffer's Cookbook Linkage Analysis course outline, from NCBI
• NIH's BIMAS linkage analysis page, including info on troubleshooting LINKAGE software error messages.
• More LINKAGE error message help here.
• Dave Curtis's lecture notes, including "Fundamental concepts in genetics" and "Methods for mapping disease genes". And the 2004 version.
• Linkage programs can be run over the web, thanks to the MRC Rosalind Franklin Centre for Genomics Research.
• easyLinkage is a graphical user interface for many linkage programs (including Mlink/Fastlink, Genehunter, and Slink) that runs on Windows and Unix machines. It might run on the Unix side of Macintosh, but I haven't tested it.
• An overview of linkage analysis, part of a training course on linkage analysis, with related exercises, from the MRC Rosalink Franklin Centre for Genomics Research.
• Notes on model-free linkage analysis (Dave Curtis)
• Lecture notes for a Statistics in Genetics course, from Terry Speed, UC Berkeley.
• Lecture notes for an Intermediate Genetics and an Advanced Genetics course, from North Dakota State Univ.

• ---

• ABI PRISM® 377 DNA Sequencer User's Manual (264-page Acrobat file, 6.1 MB) Read chapters 2 and 3 of this, about pouring and running a gel.
• Download a free version 3.1.2 updater for ABI's GeneScan software, to allow it to work with MacOS 9.
• Search or browse Applied Biosystems' document library.
• Research Genetics is now part of Invitrogen, from whom you can still buy their MapPairs
• The Sanger Centre : Human Genome Project
• Marshfield Center for Medical Genetics
• Southampton Summary Maps (old)
• UDB, The Unified Database
• NCBI HomePage
• Whitehead Institute Center for Genome Research
• Whitehead's STS search page
• Online Mendelian Inheritance in Man
• CHLC home page
• GÉNÉTHON Home Page
• CEPH marker search
• Linkage Home Page, Rockefeller Univ.
• Cookbook Linkage Analysis
• LINKAGE: User's Guide
• FASTLINK home page
• Linkage Trouble Shooting - FASTLINK/Linkage/Unknown Messages
• Web-PREPLINK
• VITESSE is a faster alternative to LINKMAP for calculating multipoint lod scores. (home page; download)
• bionet.genetic-linkage newsgroup archives
• GENE-LINKAGE FREQUENTLY-ASKED-QUESTIONS
• Human.txt from ResGen.
• links for Genetic Linkage Analysis
• Human Genome links
• Map Functions
• A nice list of linkage and mapping software from the Weizmann Institute.
• The HUGO Gene Nomenclature Committee. Use this page to search for approved gene symbols. (For instance, CCL2 is recommended now over the outdated symbol SCYA2 for chemokine (C-C motif) ligand 2.)

Marker lists

• A spreadsheet I put together listing all ABI dye-labeled markers, in all 80-odd panels, arranged by Marshfield map position. Also includes info on size range and dye. Useful when ordering new markers to cover an interesting region. Created May, 2001; may be somewhat outdated. Order individual markers from www.appliedbiosystems.com, P/N 4329191, $52.50/tube (300 rxns), "Human Linkage Mapping v2.5 Primer Pairs". Specify chromosome, panel, and marker name.
• My spreadsheet listing markers that can be ordered from ResGen, sorted by Marshfield map position. Created September 2000; may be somewhat outdated. Double-check before ordering at www.resgen.com.

allele frequencies

• Estimating Allele Frequencies using ILINK
• Genethon allele freq FTP
• ALLELE FREQUENCIES
• ALFRED: gene frequency database
• a list of sites from Univ. of Pittsburgh

References to use for linkage analysis software

We currently use version 4.0P of FASTLINK along with version 5.1 of the LINKAGE package. (These run transparently under mlinker.) For multipoint analysis, we use version 1.0 of Vitesse.

For LINKAGE:
• G. M. Lathrop, J.-M. Lalouel, C. Julier, and J. Ott, Strategies for Multilocus Analysis in Humans, PNAS 81(1984), pp. 3443-3446.
• G. M. Lathrop and J.-M. Lalouel, Easy Calculations of LOD Scores and Genetic Risks on Small Computers, American Journal of Human Genetics, 36(1984), pp. 460-465.
• G. M. Lathrop, J.-M. Lalouel, and R. L. White, Construction of Human Genetic Linkage Maps: Likelihood Calculations for Multilocus Analysis, Genetic Epidemiology 3(1986), pp. 39-52.

For Fastlink:
• R. W. Cottingham Jr., R. M. Idury, and A. A. Schaffer, Faster Sequential Genetic Linkage Computations, American Journal of Human Genetics, 53(1993), pp. 252-263. (PDF)
• A. A. Schaffer, S. K. Gupta, K. Shriram, and R. W. Cottingham, Jr., Avoiding Recomputation in Linkage Analysis, Human Heredity, 44(1994), pp. 225-237.
(PDF)

For Vitesse:
• O'Connell JR, Weeks DE. The VITESSE algorithm for rapid exact multilocus linkage analysis via genotype set-recoding and fuzzy inheritance. Nat Genet. 1995. 11:402-8.

For Pedcheck:
• O'Connell JR, Weeks DE, PedCheck: A program for identifying genotype incompatibilities in linkage analysis, Am J Hum Genet 63:259-266

For Molscript (protein-model-drawing software):
• Per J. Kraulis, "MOLSCRIPT: A Program to Produce Both Detailed and Schematic Plots of Protein Structures", Journal of Applied Crystallography (1991) vol 24, pp 946-950.