HUM-MOLGEN archive: CALL: 11q, CF, Gene Therapy (2x), 12q13

Note from the editor: This CALL message contains five submessages, about: 1) help on chromosome 11q markers 2) help in cystic fibrosis 3) graduate student looking for PhD in gene therapy (University in Europe) 4) oncologist looking for job (training) in gene therapy (in USA ?) 5) REPLY on CHR12q13 inquiry The CALL TOPIC is open for FREE CALLS for assistance, collaborations, and offerings of help in the field of Human Genetics. Please state and specify your CALL as precisely as possible, and include your name, institution and E-mail adress at the bottom of the message. Your CALL now (19-04-1995) directly reaches over 730 colleagues! Good CALLS, :-) Arthur Bergen (editor and listowner) ****************************************************************** From: MIKE OWEN <WPCMJO@CARDIFF.AC.UK> Subject: call: chromosome 11q markers I am trying to identify STRPs in the region of CRYA2 and D11S910 on chromosome 11q. Can anyone help? Mike Owen ******************************************************************* From: "Margarita I. Terrassa" <miterras@MAILBOX.SYR.EDU> Subject: CYSTIC FIBROSIS Currently, I am doing a paper on Cystic Fibrosis. However, there is so much information on the molecular studies done that it is becoming a nightmare to narrow it down. My paper has to do with the molecular techniques used in the discovery of the disease and what is being done curretly. I am writing to see if anyone can give me suggestions of which studies to concentrate on? Also, I wanted to know more about what is being done with respect to gene therapy? Who are the ones concentrated on it? Thanks, Margarita ********************************************************************** Subj: Looking for some univercities From: Georgantelis John <johnge@PROMETHEUS.HOL.GR> Hello, My name is John Georgantelis. I have a friend who wants some information about postgraduate studies in Molecular Biology. Here is his concern: My name is Takis Athanasopoulos. I have finished the Biology Dept. in the Univercity of Patras in Greece. I gain an IKY scholarship. I' m interested to get a PhD in Gene Theraphy (especially for cancer). I have C grade in my University diploma. I would appreciate your advice on selecting an appropriate Univercity in Europe that is specialized in cancer research. My foreign language is English only :) . It would be very helpful if you can write me the post and internet addresses of these univ. Thanks in advance John ****************************************************************************** From: IN%"jegmezn@ibm.net" "Jesus R Gomez-Navarro" 15-APR-1995 01:40:32.20 Subj: CALL: Oncologist looking for gene therapy training Reply-to: Jesus R Gomez-Navarro <jegmezn@ibm.net> European, 30-years-old medical oncologist; MD degree from the Facultad de Medicina, Universidad Complutense, Madrid, Spain and Board Certified as a Medical Oncologist. In 1993, I completed the residency and, immediately, got a position as Attending Physician in a hospital of the National Health System. Also working in a Ph.D. Program and doctoral thesis (epidemiological: I love computers) due to be presented in the third quarter of 1995. As my skepticism about current therapies grows, I feel more and more determined to participate in the tremendously stimulating research on gene therapy. I know this is precisely what I want, *whatever* the effort. I have experience exclusively in clinical research. No lab, no genes, no DNA (until now). But I am convinced that I need to have a good (operative) knowledge of that fields to continue my career as an oncologist next century. And this, I can not fulfill just now in Spain. Here, clinical care and research is entirely dissociated of lab research. So, which are my GENERAL OBJECTIVES? 1. Research leading to gene therapy of neoplastic disorders. 2. To translate insights in new basic and preclinical research into therapeutic advances in the gene therapy area. 3. To be in contact with groups of highly experienced clinical and preclinical investigators who have the technical capabilities to study new agents in early clinical trials. 4. To live some years abroad, particularly (but not exclusively) USA: the earth is a small planet, but my country is even smaller. And my INTEREST AREAS? 1. Vectors (any vehicle designed to deliver genetic material into human somatic cells) for the prevention, treatment, and cure of cancer through gene therapy. I like to think in vectors with similar spreading capacities to that of the metastatic cells, because those cells and its location must be strict priority. 2. Genes critical in the metastatic cascade. There are many genes involved in that chain of steps, but perhaps we can block it attacking only one or two of them. 3. Recombinant DNA (until now as a bookish hobby) 4. And of course, I am a clinician and enjoy practicing with compassion and a high ethical standard. Not specific, but I am not an expert. I know of some potential FINANCIAL aid sources to study/housing/living, so I it can not be a critical obstacle. Obviously, I must demonstrate a host investigator and project. I firmly believe that it is impossible not to find an appropiate place for my wants. PLEASE CONSIDER if you can make this real. Would you give me some specific advice about where and with whom could I train and work?. Please pass this letter to anyone possibly interested. Thank you very much in advance. Jesus R Gomez-Navarro, MD San Carlos 4, 2& esc., 3'-C 09003 Burgos Spain E-mail: jegmezn@ibm.net Phone/Fax: 34-47-27 4201 (Spain-Province-Number) ********************************************************************** Subj: CALL: REPLY: Markers on 12q13 Here is some information that may help the following enquiry: =============================================================== To everybody, I am looking for makers of any kind (VNTR, CA, STS, etc.) near the aquaporin gene on chromosome 12q13 region. Any help will be appreciated. Thank you Martin Daoust =============================================================== I include below search results from GDB for the 12q13 region, giving loci, polymorphism and probe details. The final part is help information relating to accessing GDB, so you can try it out yourself! Cheers, Martin NNNN NN Martin A Kennedy (E-mail = mkennedy@chmeds.ac.nz) ZZZZZZZ NN NN NN Cytogenetic and Molecular Oncology Unit ZZZ NN NN NN Christchurch School of Medicine ZZZ NN NNNN Christchurch, New Zealand ZZZZZZZ Phone (64-3)364-0880 Fax (64-3)364-0750 8< ======================= cut here ======================= >8 SEARCH RESULTS FOR '12Q13' Entries are preceded by a score and size. Score is scaled from 1 to 1000, and is a relative rating suggesting the appropriateness of each document with respect to the given query. 1000 1069 Locus: G00-137-135 : B12P1 : 12q13, CY122, der(12)t(12;16)(q13;q21) : 12q13[1] 630 2810 Locus: G00-119-694 : LRP1 : low density lipoprotein-related protei+ : 12q13-q14[2] 630 2858 Locus: G00-119-988 : GLI : glioma-associated oncogene homolog (zi+ : 12q13[3] 630 2120 Locus: G00-128-102 : DDIT3 : DNA-damage-inducible transcript 3 : 12q13.1-q13.2[4] 593 1055 Locus: G00-119-151 : FRA12A : fragile site, folic acid type, rare, f+ : 12q13.1[5] 593 838 Locus: G00-119-416 : MSK27 : antigen identified by monoclonal antib+ : 12q13-qter[6] 593 763 Locus: G00-119-426 : MSK36 : antigen identified by monoclonal antib+ : 12q13-qter[7] 593 837 Locus: G00-119-430 : MSK7 : antigen identified by monoclonal antib+ : 12q13-qter[8] 593 920 Locus: G00-119-453 : TAC3 : tachykinin 3 (neuromedin K, neurokinin+ : 12q13-q21[9] 593 1312 Locus: G00-119-880 : ERBB3 : avian erythroblastic leukemia viral (v+ : 12q13[10] 593 2085 Locus: G00-120-101 : WNT1 : wingless-type MMTV integration site 1,+ : 12q13[11] 593 1370 Locus: G00-120-134 : LALBA : lactalbumin, alpha- : 12q13[12] 593 1210 Locus: G00-125-357 : HMR : hormone receptor (growth factor-induci+ : 12q13[13] 593 2406 Locus: G00-126-426 : RARG : retinoic acid receptor, gamma : 12q13[14] 593 1219 Locus: G00-127-388 : HNRPA1 : heterogeneous nuclear ribonucleoprotei+ : 12q13[15] 593 1596 Locus: G00-127-453 : SP1 : Sp1 transcription factor : 12q13[16] 593 1519 Locus: G00-128-054 : SAS : sarcoma amplified sequence : 12q13-q14[17] 593 999 Locus: G00-128-288 : HPV18I2 : human papilloma virus (type 18) integr+ : 12q13[18] 593 1537 Locus: G00-128-601 : ITGB7 : integrin, beta 7 : 12q13.1[19] 593 1266 Locus: G00-128-984 : CDK2 : cyclin-dependent kinase 2 : 12q13[20] 593 1194 Locus: G00-132-336 : GSTPP : glutathione S-transferase pi pseudogene : 12q13-q14[21] 593 1195 Locus: G00-132-338 : : : [22] 593 1031 Locus: G00-134-447 : D12S117 : DNA Segment, single copy probe LL12NCO+ : 12q13.2-q13.3[23] 593 1030 Locus: G00-134-448 : D12S118 : DNA Segment, single copy probe LL12NCO+ : 12q13[24] 593 1262 Locus: G00-134-450 : D12S120 : DNA Segment, single copy probe LL12NCO+ : 12q13.1-q13.2[25] 593 1727 Locus: G00-134-461 : D12S131 : DNA Segment, single copy probes LL12NC+ : 12q13[26] 593 1692 Locus: G00-134-467 : D12S137 : DNA Segment, single copy probes LL12NC+ : 12q13.2-q13.3[27] 593 1262 Locus: G00-134-479 : D12S149 : DNA Segment, single copy probe LL12NCO+ : 12q13-q15[28] 593 1030 Locus: G00-134-499 : D12S169 : DNA Segment, single copy probe LL12NCO+ : 12q13.3-q14[29] 593 1199 Locus: G00-134-504 : D12S174 : DNA Segment, single copy probes LL12NC+ : 12q13[30] 593 1030 Locus: G00-134-505 : D12S175 : DNA Segment, single copy probe LL12NCO+ : 12q13.1-q14[31] 593 1030 Locus: G00-134-506 : D12S176 : DNA Segment, single copy probe LL12NCO+ : 12q13.1-q14[32] 593 1174 Locus: G00-136-424 : HEM1 : hematopoietic protein 1 : 12q13.1[33] 593 1032 Locus: G00-136-986 : D12S185 : DNA Segment, single copy probe LL12NC0+ : 12q13.2-q14[34] 593 1496 Locus: G00-136-992 : D12S191 : DNA Segment, single copy probes LL12NC+ : 12q13.3-q14[35] 593 1031 Locus: G00-136-999 : D12S198 : DNA Segment, single copy probe LL12NC0+ : 12q13.1-q13.3[36] 593 1031 Locus: G00-137-006 : D12S205 : DNA Segment, single copy probe LL12NC0+ : 12q13.1-q13.3[37] 593 1032 Locus: G00-137-017 : D12S216 : DNA Segment, single copy probe LL12NC0+ : 12q13.3-q15[38] 593 1031 Locus: G00-137-027 : D12S226 : DNA Segment, single copy probe LL12NC0+ : 12q13.2-q13.3[39] 1 9789 Help information on database: gdb-locus[40] Total Hits: 40 SEARCH RESULTS FOR '12Q13' Entries are preceded by a score and size. Score is scaled from 1 to 1000, and is a relative rating suggesting the appropriateness of each document with respect to the given query. 1000 1552 Polym: G00-156-290 : GLI/A : UNKN : het 0.40[1] 1000 1134 Polym: G00-156-408 : WNT1/A : UNKN[2] 1000 1799 Polym: G00-210-992 : D12S371/A : DINUC : het 0.84[3] 1000 1616 Polym: G00-250-945 : LRP1/A : TETNUC : het 0.58[4] 1000 1895 Polym: G00-305-076 : D12S766/A : DINUC : het 0.34[5] 1000 1867 Polym: G00-305-098 : D12S131/A : DINUC : het 0.30[6] 1000 1953 Polym: G00-305-104 : D12S137/A : DINUC : het 0.76[7] 1000 1954 Polym: G00-305-113 : D12S262/A : DINUC : het 0.76[8] 1000 1925 Polym: G00-305-122 : D12S191/A : DINUC : het 0.80[9] 1 9789 Help information on database: gdb-polym[10] Total Hits: 10 SEARCH RESULTS FOR '12Q13' Entries are preceded by a score and size. Score is scaled from 1 to 1000, and is a relative rating suggesting the appropriateness of each document with respect to the given query. 1000 1468 Probe : G00-364-429 : 272g5 : Cloned Genomic : D12S1019, GLI[1] 1000 1374 Probe : G00-364-430 : 142f5 : Cloned Genomic : D12S1020, GLI[2] 1000 1381 Probe : G00-364-431 : A2MR_cDNA : Cloned cDNA : D12S1021, LRP1[3] 858 1481 Probe : G00-163-925 : pAL1 : Cloned Genomic : WNT1 (+)[4] 858 1270 Probe : G00-165-890 : cKK36P1 : Cloned Genomic : GLI(+)[5] 858 1211 Probe : G00-168-147 : LALBA.Clone2 : Cloned Genomic : LALBA[6] 858 1303 Probe : G00-168-148 : LALBA.Clone1 : Cloned cDNA : LALBA[7] 858 1475 Probe : G00-172-401 : pGT3.1 : Cloned cDNA : GSTPP[8] 858 1695 Probe : G00-173-363 : LRP-6, LRP06 : Cloned cDNA : LRP1[9] 858 1247 Probe : G00-179-276 : RARg1 : Cloned cDNA : RARG[10] 858 1319 Probe : G00-179-277 : RAR-gene3 : Cloned Genomic : RARG[11] 858 1200 Probe : G00-179-278 : RAR-gene1 : Cloned Genomic : RARG[12] 858 1323 Probe : G00-179-279 : RAR-gene2 : Cloned Genomic : RARG[13] 858 1211 Probe : G00-179-615 : rhA20 : Cloned cDNA : RARG[14] 858 1201 Probe : G00-179-616 : rhB43 : Cloned cDNA : RARG[15] 858 1217 Probe : G00-180-862 : pE3-16 : Cloned cDNA : ERBB3[16] 858 1242 Probe : G00-180-863 : ERBB3.e3-1 : Cloned Genomic : ERBB3[17] 858 1167 Probe : G00-181-186 : HMR.N10 : Cloned cDNA : HMR[18] 858 1222 Probe : G00-181-392 : ITGB7.P7 : Cloned cDNA : ITGB7[19] 858 1222 Probe : G00-181-393 : ITGB7.P2 : Cloned cDNA : ITGB7[20] 858 1218 Probe : G00-181-476 : pRP18 : Cloned cDNA : HNRPA1[21] 858 1254 Probe : G00-181-791 : lambda8.1 : Cloned Genomic : HNRPA1[22] 858 1234 Probe : G00-181-792 : lambda1.7 : Cloned Genomic : HNRPA1[23] 858 1231 Probe : G00-181-794 : SP1.1 : Cloned cDNA : SP1[24] 858 1306 Probe : G00-182-384 : pNV7-CDK2 : Cloned cDNA : CDK2[25] 858 1221 Probe : G00-186-531 : pMe51 : Cloned cDNA : HMR[26] 858 1228 Probe : G00-186-663 : RAB5B.1 : Cloned cDNA : [27] 858 1197 Probe : G00-186-664 : RAB5B.2 : Cloned Genomic : [28] 858 1189 Probe : G00-186-665 : RAB5B.3 : Cloned Genomic : [29] 858 1269 Probe : G00-188-742 : pHER3-3b : Cloned cDNA : ERBB3[30] 858 1192 Probe : G00-190-491 : LL12NCOIN-1C11 : Cloned Genomic : D12S117[31] 858 1191 Probe : G00-190-492 : LL12NCOIN-1C2 : Cloned Genomic : D12S118[32] 858 1191 Probe : G00-190-494 : LL12NCOIN-1C4 : Cloned Genomic : D12S120[33] 858 1191 Probe : G00-190-505 : LL12NCOIN-1D7 : Cloned Genomic : D12S131[34] 858 1192 Probe : G00-190-511 : LL12NCOIN-1B12 : Cloned Genomic : D12S137[35] 858 1191 Probe : G00-190-523 : LL12NCOIN-2D1 : Cloned Genomic : D12S149[36] 858 1191 Probe : G00-190-543 : LL12NCOIN-5H3 : Cloned Genomic : D12S169[37] 858 1191 Probe : G00-190-548 : LL12NCOIN-1B6 : Cloned Genomic : D12S174[38] 858 1191 Probe : G00-190-549 : LL12NCOIN-1B8 : Cloned Genomic : D12S175[39] 1 9789 Help information on database: gdb-probe[40] Total Hits: 40 =============================================================================== Address any questions regarding the Genome Data Base (GDB) to: help@gdb.org GDB is also accessible as a relational database. For more information, send mail to help@gdb.org or call (410) 955-9705. GDB is supported by the U.S. Department of Energy and the U.S. National Institutes of Health, and is hosted at the Johns Hopkins University School of Medicine. Johns Hopkins University makes no warranty (express, implied, or statutory) regarding GDB or any data stored within it, including without limitation implied warranties of merchantability, fitness for use, or fitness for a particular purpose. =============================================================================== ABOUT THIS HELP DOCUMENT This document explains what you will find in the GDB databases, and how to construct a query. This document is always returned when you issue a query to one of the GDB databases. It is the only document returned if your query produces no results. This document was last updated on May 12, 1994. =============================================================================== 1. GDB databases available through WAIS: There are 9 GDB sources listed in the directory-of-servers: gdb-cell-line.src gdb-citation.src gdb-contact.src gdb-library.src gdb-locus.src gdb-map.src gdb-mutation.src gdb-polym.src gdb-probe.src Here is a brief description of each: gdb-cell-line.src ----------------- Clonal mammalian cell lines which are useful for genomic mapping research. Cell line descriptions include the name and type of the cell line, the chromosomal breakpoints it contains and information on how to obtain the cell line (accession numbers for the ATCC and Coriell repositories, and contact information). gdb-citation.src ---------------- Bibliographic citations (often with abstracts) for all GDB data. Citations in GDB include journal articles, books, book chapters, meeting abstracts and personal communications. The citation record also includes a list of linked GDB objects. gdb-contact.src --------------- Contact information for researchers involved in genome mapping, as well as GDB editors and staff. The contact record includes name, address, phone and fax numbers and email address. Where the contact has submitted clones, cell lines or libraries to GDB, these are also shown in the record. gdb-library.src --------------- Collections of DNA clones, often from specific regions of the genome, useful for mapping research. The library description includes the library name, type of cloned DNA, type of vector used to construct the library, contact information (for researchers and national repositories) and a list of clones isolated from the library. gdb-locus.src ------------- Defined regions of the genome, ranging in size from a single point to an extended region. Locus types in GDB include genes, DNA segments, fragile sites and breakpoints. Locus descriptions include cytogenetic location, official name and symbol, mapping method(s) used and pointers to related GenBank sequence database entries and OMIM documents. gdb-map.src ----------- Genetic or physical maps representing an ordered set of elements (loci or probes) on a chromosome. Each map is a string of locus or probe symbols separated by delimiters which indicate the relationship between neighboring elements. Included in the database are maps produced from primary experimental observations, and maps derived from a consensus of several primary maps. Map descriptions include the mapping method used, a summary map location, information about the loci or probes in the map and the distances between map objects, where available. gdb-mutation.src ---------------- Less common sequence variations in loci, often responsible for clinical phenotypes. Mutation descriptions include the type of mutation, location within the gene and comparison of wildtype and mutant DNA and protein sequences. gdb-polym.src ------------- Common variations in the DNA sequence of loci, often useful in genetic mapping experiments. Polymorphism descriptions include the type of variation, the methods used to detect the polymorphism, and the nature and frequency of the alleles observed in the populations studied. gdb-probe.src ------------- Reagents for detecting genes, DNA segments and their variation. Probe types include cloned, PCR (Polymerase Chain Reaction) and ASO (Allele Specific Oligonucleotide) probes. Probe descriptions include information about the loci detected by the probe, contacts for obtaining the probe, the probe DNA type, vector information (for cloned probes) and primer sequences (for PCR and ASO probes). GDB WAIS is updated weekly during off-peak hours. If you attempt to search the database during an update, you may receive a message stating that an update is in progress. Please retry your search an hour or so later. 2. Content of GDB documents Each document contains a detail section, with information specific to the object selected. Many documents also contain single line "links" to other objects in the database. For example, a "contact" document contains name and address information, and optionally, links to "probe" documents. A "link line" contains the unique GDB Id of the object, which provides a means of retrieving that document. For example, here is a "probe link line" which appears in a "contact" document: Probe Name Type DNA Type Locus GDB Id ---------------------------------------------------------------------- ERBB3.e3-1 Cloned Genomic ERBB3 G00-180-863 To retrieve this probe document, you first add "gdb-probe.src" to your list of sources, then type "G00-180-863" (omit the quotes, see below) in the query box. Every headline contains the GDB Id of the object, so you can easily select the specific probe document from the list of headlines returned. Note: do not put a GDB Id in quotes, i.e., "G00-180-863". Any word in quotes is interpreted literally; unfortunately, the presence of the hyphens in a GDB Id causes the Id to be interpreted as 3 separate words. 3. Searching Strategies Note: the WAIS server is case insensitive! The following queries are identical: "duchenne muscular dystrophy" "DUCHENNE MUSCULAR DYSTROPHY" "dUcHeNnE mUsCuLaR dYsTrOpHy" a. Be Specific Avoid using keywords which occur frequently. The GDB databases contain over 150,000 documents. The more specific you are when supplying a query, the more relevant the titles returned will be. Warning! Many common words are ignored. The following query: gene will return NO results because the word "gene" occurs so frequently that it is not contained in the index of keywords. Instead, name the gene, or describe it if you don't know the name. CFTR ADA-deficient severe combined immunodeficiency disease b. Use Booleans when Possible By default, the query words are treated as if the word "OR" appears between each. For example, the following queries terms are identical: Kramer Minty Kramer OR Minty retrieves the documents which contain the words (in this case, authors) Kramer OR Minty. The query: Kramer AND Minty retrieves only one document, which includes citations for articles written by both Kramer and Minty. The boolean "NOT" can be used to refine a search even further. The query: heavy AND polypeptide NOT ferritin looks for documents that include the words "heavy" and "polypeptide" but NOT the word "ferritin". c. Use Quotes to Narrow Your Search The query above in example "b" might locate documents which are in fact not about "heavy polypeptides", because the words "heavy" and "polypeptide" can occur independently of each other in the document. Quotes can be used around the phrase, however, so a more specific form of the query is: "heavy polypeptide" NOT ferritin The quoted phrase is searched for in the exact form as it is specified. d. Use the Asterisk Wildcard to Broaden Your Search If you want to search for all the locus records which mention any genes on the short arm of chromosome 15, for example, you can specify the following query: 15p* You CANNOT include the asterisk wildcard within a quoted phrase, because everything within the quotes is interpreted literally. This query returns no documents: "15p*" The asterisk wildcard can only be used at the END of a word, so the following query also returns no document: 15p*22 ========================== End of Help Document ============================= GDB[1]