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Purchase

Feb 14, 2013   //   by Peter Rogan   //    //  No Comments

1. Subscription:  Automated Splice Site and Exon Definition Analysis Server

If your guest access to the ASSEDA server has been exhausted, you have been automatically directed here to the Cytognomix website.  The server is described in our recent paper, “Prediction of Mutant mRNA Splice Isoforms by Information Theory-Based Exon Definition.”  You may obtain  an subscription through our secure Paypal account which provides unrestricted access to the site. The annual fee is $200 (plus applicable taxes), which entitles you to unrestricted use of the server for 365 days*. Please provide your account Email address below and payment information as requested. We will notify you by Email when the guest account has been converted to a subscription.

Registered email address

*ASSEDA and the backup server are generally available 24/7, however we cannot assure 100% uptime

2. Software: Shannon pipeline plug-in for mRNA splicing mutation analyis

This product is available either as a stand-alone workbench or remote server versions from our distributor, CLC bio.

Careers

Oct 20, 2012   //   by Peter Rogan   //    //  No Comments

Located in the London Ontario, Cytognomix Inc. offers employees rewarding and challenging careers in an exciting, evolving market. Quite simply, Cytognomix  is a pioneer in the genomics and genome bioinformatics industry.

We welcome new employees with a pioneering spirit. Fresh ideas. Different perspectives. Creative minds.

Experience in software development, bioinformatics, genome-scale thinking are sought.

Cytognomix is growing in a variety of areas.  Currently there are no open positions at Cytognomix.

CEO on Facebook

Jun 30, 2012   //   by Peter Rogan   //    //  No Comments

Peter K Rogan

Create Your Badge“>

Cytognomix receives new US Patent

Jun 26, 2012   //   by Peter Rogan   //    //  No Comments

US patent (8,209,129) was issued today on Single Copy DNA probes that include divergent repetitive sequences, thus extending the portions of the genome that can be used for such probes beyond traditional single copy sequences. The technology also increases the density of genomic DNA probes for higher resolution genetic analysis beyond what is used in FISH, genomic microarrays for array comparative genomic hybridization, and solution capture hybrdization arrays for sequence enrichment in deep sequencing. The patent has been licensed to Cytognomix.

Products

May 24, 2011   //   by Peter Rogan   //    //  No Comments

Shannon pipeline:

Genome-scale interpretation of mutations (Try it now!)

manhattan-like plot

Software to predict splicing mutations along a chromosome

 

 

 

 

 

 

 

 

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About Us

May 24, 2011   //   by Peter Rogan   //    //  No Comments

Cytognomix is a London, Ontario based biotechnology company developing software-based solutions and reagents for clinical genomics. The company has a significant intellectual property portfolio, which emphasizes products for clinical diagnostic applications. Current products include mutation interpretation software, DNA probe reagents and companion software to detect chromosome abnormalities at the molecular level.

Cytognomix’s proprietary Single Copy (sc) technology brings precise, sensitive, and informative genetic disease management tools to advanced clinical laboratories for detection of chromosome anomalies related to genetic disease. Cytognomix designs and produces molecular cytogenetic tests using fluorescent in-situ hybridization scFISH probes. In addition, microarray-based comparative genomic hybridization (aCGH) can use SC technology to increase reproducibility and reduce cost per sample. A key Cytognomix tool is our proprietary genome browser interface that simplifies selection of single copy probes for nearly any gene-mapped disease. Cytognomix’s scFISH probes will assure correct diagnosis and make possible more personalized treatment than conventional approaches.

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Applications

Intellectual Property

Management

Technology

Subtelomeric SC-FISH probes Catalog(Continued)

May 18, 2011   //   by Peter Rogan   //    //  No Comments
 

Chr. Target  

scFISH probes1 

Competitor Recombinant probes2
Catalog Number Chr
Length(bp)
Distance from Telomere (kb)3 

Estimated clone size
Approx distance of STS from telomere (kb)4
ST-0000131 8ptel 2271 455.377 – 457.645
2154 71.870 - 74.023 100 kb6 194 ± 100
ST-0000132 8qtel
ST-0000133 8qtel 2949 145.868 – 148.816
ST-0000134 9ptel 1754 243.057 – 244.809 115 kb 140 ± 1159
ST-0000135 9qtel 2232 248.993 – 251.226 95 kb 223 ± 95
ST-0000136 9qtel 2707 231.636 – 234.340
ST-0000137 9qtel 2278 257.634 – 259.785
ST-0000138 10ptel 2132^+ 363.852 – 365.942 80 kb6 328 ± 80
ST-0000139 10ptel 2051+ 320.896 – 322.898
ST-0000140 10ptel 3203+ 282.669 – 285.872
ST-0000141 10ptel 2526^+ 151.566 – 154.092
1820 75 kb 193 ± 75
ST-0000142 10qtel 184.961 – 186.780
ST-0000143 11ptel 2884 1,205.118 - 1,208.002 110 kb6 290 ± 110
2489*
ST-0000144 11ptel 66.589 – 69.078
2462 1,781.588 - 1,784.049 160 kb unknown
ST-0000145 11qtel
ST-0000146 11qtel 2026* 33.471 – 31.445
1914 100 kb 0-209
ST-0000147 12ptel 180.472 – 182.385
3456 165 kb 180 ± 165
ST-0000148 12qtel 154.406 – 157.861
ST-0000149 13qtel 3209 366.172 – 369.380 75 kb 2,900 ± 75
ST-0000150 14qtel 1866 3,155.170 - 3,157.035 160 kb (4,100-4,200) ± 117
ST-0000151 14qtel 3839 3,128.031 - 3,131.869
ST-0000152 14qtel 1984* 1,022.102 – 1,020.118
ST-0000153 14qtel 2617* 1,019.175 – 1,016.558
ST-0000154 15qtel 1607 131.552 – 133.158 100kb 420 ± 100
ST-0000155 16ptel 3361* 73.825 – 77.186 110 kb 3056± 110
2082*
ST-0000156 16ptel 56.610 – 58.692
2567 110 kb6 210 ± 110
ST-0000157 16qtel 183.506 – 186.072
ST-0000158 17ptel 2593 895.021 – 897.613 70 kb6 105 ± 70
ST-0000159 17ptel 4984 859.347 – 864.330
2219*
ST-0000160 17ptel 101.957 – 104.176
6191*
ST-0000161 17qtel 106.452 – 100.262
3026 160 kb 750 ± 160
ST-0000162 17qtel 848.341 – 871.383
2530 80.057 170 kb (154-285) ± 40
ST-0000163 18qtel - 82.584
ST-0000164 19ptel 1815 1,745.686 - 1,747.500 80 kb unknown
ST-0000165 19ptel 2094 1,721.659 - 1,723.752
2400*
ST-0000166 19ptel 265.605 – 268.005
4137*
ST-0000167 19ptel 249.688 – 253.825
2721 121.866 160 kb 244 ± 160
ST-0000168 19qtel - 124.586
ST-0000169 19qtel 2399 88.475 - 90.874
ST-0000170 20ptel 2616 365.951 - 368.566 160 kb 0-240
3133 109.581 140 kb 62-202
ST-0000171 20qtel - 112.713
ST-000172 20qtel 3695 114.557 - 118.251
ST-0000173 20qtel 2166 140.088 - 142.253
ST-0000174 20qtel 2997 186.460 - 189.456
ST-0000175 21qtel 4370 47.861 - 52.230 170 kb 0-337
ST-0000176 22qtel 3550 176.274 - 178.618 80 kb (161-168) ± 73
ST-0000177 Xptel 1896 2,329.080 - 2,330.975 175kb 324 ± 175 (X,Y homology)8
3700*
ST-0000178 Xptel 155.557 – 159.257
2529 645.399 170kb 0-258
ST-0000179 Xqtel - 647.927
ST-0000180 Yptel 2446 2,562.365 - 2,564.810 175kb Unknown (X,Y homology)8
ST-0000181 Yptel 2000 2,567.816 - 2,569.815 170kb

Patent Information

Previous Page

1 scFISH probes developed from April 2003 genome draft are labeled with asterisk (*). The remaining probes were from April 01 draft except 1p (Nov 02), 2q, 3q, 4p, 5p, 6, 8q, 9p (June 02). Sequence IDs corresponding to these probes contain the UCSC database version number in the descriptions of these products.
2 Many of conventional FISH probes were developed by Knight et al. Am. J. Hum. Genet. 67: 320, 2000, and by Abbott Laboratories/Vysis, Inc.
3Distance from probe to end of the telomere reported in this table is based on the length of the interval from the probe boundary coordinates to the terminal nucleotide coordinates of each chromosome end in the April 03 version of genome sequence. The computer program BLAT at the Genome Browser website (genome.ucsc.edu) was used to determine these coordinates. Due to inaccuracy in the BLAT algorithm, the coordinates of probe boundaries may differ from the actual coordinates slightly.
4 The position of STS/ marker associated with the conventional FISH probe was determined in the April 03 version of the genome sequence. Often a single STS/ marker is identified on a clone. There is insufficient information available to determine the positions of STS markers on some of these clones. As a result, error in positioning a probe on the chromosome (ie. ± ) is generally the size of the clone provided in: American Journal of Human Genetics 67: p. 320, 2000, and by Abbott/Vysis, Inc . A standard deviation less than the estimated clone size indicates that more than one STS was localized to the clone.
6 Indicates clones with cross hybridizations to other chromosomes.
7 Probe recognizes a neighboring paralogous sequence in addition to the known interval.
8 Reported STS located on X chromosome only, but both commercial probes for sex chromosomes show homology with each other.
9 Probe detect four paralogs: three of which are on chromosome 9 and one which is on chromosome 2.
unknown = Reported STS/ markers could not be placed on genome sequence as they could not be located in all available genome databases or through communication with authors.
^hybridization was detected when probe was combined with other 10ptel probes labeled with “^”.
+ hybridization was detected when probe was combined with other 10ptel probes labeled with “+”.

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Subtelomeric SC-FISH probes Catalog

May 18, 2011   //   by Peter Rogan   //    //  No Comments
 

Chr. Target  

scFISH probes1 

Competitor Recombinant probes2
Catalog Number Chr
Length(bp) Distance from Telomere (kb)3 

Estimated clone size Approx distance of STS from telomere (kb)4
ST-0000101 1ptel 2531* 1,045.411 – 1,047.942 90 kb unknown
3930* 1,048.515 – 1,052.445
ST-0000102 1ptel
3512* 1,053.361 – 1,056.873
ST-0000103 1ptel
2671 3,858.025 - 3,860.694
ST-0000104 1ptel
1853 7,939.921 - 7,941.773 100 kb 236 ± 100
ST-0000105 1qtel
ST-0000106 1qtel 1632* 97.847 – 96.215
2503 89.194-86.692
ST-0000107 1qtel
2653 175 kb 322 ± 175
ST-0000108 2ptel 112.585 – 115.237
3355 2,398.933 - 2,402.287 60 kb 390 ± 46
ST-0000109 2qtel
ST-0000110 3ptel 2093* 181.265-183..325 80 kb 248 ± 80
1834* 199.161-200..994
ST-0000111 3ptel
2953 762.774 - 765.726 95 kb6 997 ± 95
ST-0000112 3qtel
2022*
ST-0000113 3qtel 595.753 – 593.731
ST-0000114 4ptel 1796 246.384 – 248.179; 417.863 – 419.7107 145 kb6 (220-292) ± 73
2426 442.967 - 445.387 130 kb 930 ± 130
ST-0000115 4qtel
ST-0000116 5ptel 2189 86.825 - 89.013 191kb unknown
2795 2,032.602 - 2,035.396 105 kb 227 ± 105
ST-0000117 5qtel
ST-0000118 5qtel 2661 2,019.454 - 2,022.114
ST-0000119 5qtel 2633* 627.290 – 624.657
ST-0000120 

 

5qtel 1753* 422.516 – 420.763
ST-0000121 6ptel 2152 199.487 - 201.638 80 kb unknown
2554 175.551 - 178.104 100 kb (276-282) ± 94
ST-0000122 6qtel
ST-0000123 7ptel 2872 815.565 - 818.439 60 kb 218 ± 59
2434*
ST-0000124 7ptel 143.257 – 145.691
2348*
ST-0000125 7ptel 146.749 – 149.097
2574 1,095.575 - 1,098.148 95 kb 225 ± 95
ST-0000126 7qtel
1517*
ST-0000127 7qtel 28.945 – 27.428
1634*
ST-0000128 7qtel 5.405 – 3.771
1865*
ST-0000129 7qtel 81.313 – 79.448
ST-0000130 8ptel 2079 483.728 – 485.805 135 kb 1,200 ± 135

 

Patent Information

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Standard Fish Probes Catalog (Continued)

May 18, 2011   //   by Peter Rogan   //    //  No Comments
Chromosome /Disorder Catalog Number GenBank Accession Gene Interval Cytogenetic nomenclature
16/AML-M4 ST-0000034 NT_000691 PM53 ~20 kb downstream ish inv(16)(p13q22)(PM5 sp)
(Acute Myelogenous leukemia – M4) ST-0000035 NT_000691 PM53 ~60 kb downstream
ST-0000036 NT_000691 PLA2G103 

PKD

PM5

IVS 3 

IVS 12-Exon 15

~100 kb upstream

ish inv(16)(p13q22)(PLA2G10 mv, PKD mv, PM5 sp)
ST-0000037 NT_000691 PLA2G103 

PKD

PM5

IVS 3 

Exon 15-IVS 20

~100 kb upstream & ~300 kb downstream

ST-0000038 NT_025903 ABCC1/MDR1 IVS 6 ish inv (16)(p13q22)(ABCC1st)
16/Ruben- stein-Taybi Sx ST-0000039 NT_000671 CREBBP IVS 19 – IVS 20 ish del(16)(p13.3)(CREBBP-)
ST-0000040 NT_000671 CREBBP IVS 19
17/Smith- Magenis Sx ST-0000041 NT_000770 ADORA2B4 Promoter-IVS 1 ish del (17)(p11.2p11.2)(ADORA2B-)
ST-0000042 NT_000770 ADORA2B4 IVS 1
ST-0000043 U80184 FLI1 IVS 12-IVS 14 ish del (17)(p11.2p11.2)(FLI1-)
ST-0000044 U80184 FLI1 IVS 15-Exon 21
ST-0000045 NT_000760 MFAP4 IVS 2 – 3 UTR ish del(17)(p11.2p11.2)(MFAP4-)
ST-0000046 AL035367 ZNF179-PAIP1; 

LLGL/HUGL;

SHMT1

Between ZNF179 PAIP1; IVS7-Exon 13; IVS 4 ishdel (17)(p11.2p11.2) (ZNF179/PAIP1/SHMT1-)
ST-0000047 AL035367 LLGL/HUGL Promoter –Exon 1 

Promoter – IVS1

ish del(17)(p11.2p11.2)(LGLL/HUGL-)
17/Charcot- 

Marie–Tooth 1A

ST-0000048 AC005703 PMP22 Promoter 

(~5 kb upstream)

ish dup(17)(p11.2p11.2)( PMP22++)
ST-0000049 AC005703 PMP22 IVS 3
ST-0000050 AC005703 PMP224 IVS 3
17/ Miller-Dieker Sx ST-0000051 NT_000774 PAFAH1B1 ~5kb downstream ish del(17)(p13.3)(PAFAH1B1/EIF-3-) 

EIF-35 IVS 24–IVS 27
ST-0000052 NT_000774 PAFAH1B1 ~7-8 kb downstream
EIF-35 

IVS 15-IVS 19
ST-0000053 NT_000774 PAFAH1B1 ~13 kb downstream
ST-0000054 EIF-35  

IVS 5-IVS 11
Alagille Sx ST-0000055 AL035456.24 JAG1 IVS 2-IVS 3 ish del(20)(p12.3p12.3)(JAG1-)
ST-0000056 AL035456.24 JAG1 IVS 5-IVS 8
21/Down Sx ST-0000057 AP000160 DSCR4 ~39 kb upstream ish (21)(q22.2q22.3)(DSCR4x3)
ST-0000058 AP000160 DSCR4 ~30 kb upstream
ST-0000059 AP000160 DSCR4 ~20 kb upstream
21/ ALL ST-0000060 AP000057 AML1/RUNX Promoter-exon 1 ish t(12;21)(p13;q22)(AML1 st)
22/ DiGeorge Sx ST-0000061 NT_001039 HIRA IVS 21-IVS 24 ish del(22)(q11.2)(HIRA-)
ST-0000062 NT_001039 HIRA IVS 13-IVS 15
ST-0000063 NT_001039 HIRA IVS 12-IVS 13
ST-0000064 NT_001039 HIRA IVS 2-IVS 4
ST-0000065
22/CML; ALL ST-0000066 U07000 BCR Proximal to major 

breakpoint in CML

ish t(9;22)(q34;q11.2)(BCR st)
ST-0000067 U07000 BCR Proximal to major breakpoint in CML
ST-0000069 U07000 BCR IVS 8 ish t(9;22)(q34;q11.2)(BCR mv)
X/ Kallman Sx ST-0000070 NT_ 001457 GS2 Promoter- IVS 2 ish del(X)(p22.31)(GS2-)
ST-0000071 AC006062 KAL1 IVS 6-IVS 7 ish del(X)(p22.31)(KAL1-)
ST-0000072 AC006062 KAL1 ~8 kb downstream
X/ Turner; Leri- Weill Sx ST-0000073 NT_001151 SHOX IVS 2- exon 3 ish del(X)(p22.33)(SHOX-)
ST-0000074 NT_001151 SHOX IVS 4
ST-0000075 NT_001151 SHOX IVS 6
ST-0000076 NT_001159 TBL1 IVS 3 ish del(X)(p22.22-22.31)(TBL1-)
ST-0000077 NT_001159 TBL1 Exon 15- 3  

 

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Standard Fish Probes Catalog

May 18, 2011   //   by Peter Rogan   //    //  No Comments

Table 1. scFISH probes used to detect cytogenetic abnormalities

Chromosome /Disorder Catalog Number GenBank Accession Gene Interval** Cytogenetic nomenclature
1/Monosomy 1p36 Sx ST-0000001 AL031282 CDC2L1 IVS 11-3 UTR ish del (1)(p36.3)(CDC2L1-)
ST-0000002 AL031282 CDC2L1 3 UTR
4/ Wolf-Hirschorn Sx ST-0000003 NT_000102 HD Exon 67 – 0.2 kb downstream ish del (4)(p16.3)(HD-)
5/Cri-du-Chat Sx ST-0000004 NT_000149 CTNND2 IVS 17 ish del (5)(p15.2)(CTNND2-)
ST-0000005 NT_000149 CTNND2 IVS 14
ST-0000006 NT_000149 CTNND2 IVS 13
ST-0000007 NT_000147 SEMA5A IVS 3 ish del (5)(p15.31)(SEMA5A-)
ST-0000008 NT_000147 SEMA5A IVS 3
ST-0000009 NT_000147 SEMA5A IVS 3
ST-0000010 AF119117 SLC6A3 IVS 3 ish del (5)(p15.33)(SLC6A3-)
7/Williams Sx ST-0000011 NT_000398 L1MK1 IVS 2 ish del(7)(q11.23q11.23)(LIMK1-)
ST-0000012 NT_000398 L1MK1 IVS 13-3UTR
8/Langer- ST-0000013 NT_002886 TRPS1 IVS 1 ish del(8)(q23.3q24.1)(TRPS1-)
Giedeon Sx ST-0000014 NT_002886 TRPS1 IVS 1
9/CML ST-0000015 U07561 ABL1 Exon 1b-IVS 1b ish t(9;22)(q34;q11.2)(ABL st)
(Chronic myelogenous leukemia) ST-0000016 U07562 ABL1 IVS 1b
ST-0000017 U07563 ABL1 IVS 3 ish t(9;22)(q34;q11.2)(ABL mv)
ST-0000018 U07563 ABL1 IVS 3
ST-0000019 U07563 ABL1 IVS 4-IVS 6 ish t(9;22)(q34;q11.2)(ABL mv)
ST-0000020 U07563 ABL1 Exon 11-IVS 11
12/ALL (Acute lymphocytic leukemia) ST-0000021 NT_000601 TEL/ETV6 IVS2 ish t(12;21)(p13;q22)(TEL sp)
ST-0000022 NT_000601 TEL/ETV6 IVS3
ST-0000023 NT_000601 TEL/ETV6 IVS5-IVS6
13/ Aneuploidy ST-0000024 AL355338 ZIC2 ~5.8 kb downstream ish del(13)(q32)(ZIC2-) or
ST-0000025 AL355338 ZIC2 ~2 kb upstream ish del(13)(q32)(ZIC2x3)
15/Prader-Willi, Angelman & Duplication Sx ST-0000026 AC004600 UBE3A IVS 8-IVS 9 ish del(15)(q11.2q11.2)(UBE3A-)
ST-0000027 AC004737 IC/SNRPN IVS 3 to Exon u1B2 ish del(15)(q11.2q11.2)(IC/ SNRPN-)
ST-0000028 U41384.1 SNRPN Promoter – IVS 1 ish dup(15)(q11.2q13)(UBE3A++,
ST-0000029 AC004737 IC/SNRPN IVS 5-Exon u1B2-IVS 3 IC/SNRPN++), and ish dic(15q11.2q13) (UBE3A++,IC/SNRPN++)
ST-0000030 AC004737 IC/SNRPN IVS 5-Exon u1B
ST-0000031 AC006596 MAGEL2 CDS- 3 UTR-2 kb downstream ish del(15)(q11.1q11.2)(MAGEL2-) or
ST-0000032 AC006596 MAGEL2 ~4 kb downstream ish dup (15)(q11.2q11.2)(MAGEL2++)
ST-0000033 AC006596 MAGEL2 ~22 kb downstream

 

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** WWW hyperlinks are to localized probe sequence in ContigView browser (v9.30a.1; 2 December 2002) at http://www.ensembl.org/Homo_sapiens/

 

 

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