Analysis 07122007 Auto Saved)

Turkish origin 025, 039, 146, 153, 156, 186, 252, 332, 350

Cut Off 25

STY Dist. telomer (Mb) start stop

Chrom

Ind. freq

2 3 5 8 centromer 11 12 12 12 16 16 21 X

1-4 2-5 2, peak4 2-5 2-4 1-4 3-4 2-5 2-4 2-4 1-3 4-7

210 30 70, peak at 80 40 15 5 50 95 9 30 18

2 3 5 8 11 12 12 12 16 16 21 X

1-3 1-3 1-2 2 1-2 1-4 3-4 2-3 2-3 2 1 4-7

195 25 25 40 10 5 55 95 10 29 18

1 2 3 5 8 11 12 12 12 16 16 21 X

2 1-3 1-2 1-2 nil 1-2 1 1-4 1-2 1-2 1-2 1 1-4

18 210 30 70 40 scattered: 10 scattered: 5 50 100 9 35 18

235 60 100 50 125 45 (centromer 35) 65 115 18 50 45

Ind. freq 1 1-4;1-5 no peak 1-5 2-4 1-4 nil; 2 2 1 1-6 nil 4-8

control start-stop peaks 220, 225 45; 50 peak 50 50 peaks 30, 45 peak 110 peaks 30, 45 30-50 all

Chrom

Ind. freq

2 3 5 8 cent 11 12 12 12 16 16 21 X

1-6 1-8 1-4 4 2-7 1-5 2-6 2-3 2-3 2-3 1 3-8

2 3 5 8 cent 11 12 12 12 16 16 21 X

1-3 1-2 0-1 1-5 1-5 1-5 2 2 2-3 1 2-5

1 2 3 5 8 11 12 12 12 16 16 21 X

1-2 1-2 1-2 1-2 nil 1-2 1 2-3 2 2 2 1 1-5

NSP Dist. telomer (Mb) start stop 210 22, peak 52 25, peak 80 40 10 peak 30, 40 5 52 95 10 27 18

240 62 100 50 50 55 (centromer 35) 65 115 22 55 45

1-3 25 25 40 10 10 50 95 10 27 18

240 60 105 50 55 120 65 115 22 55 45

18 210 25 50 40 scattered: 10-53 and scattered: 12 52 100 7 48 18-28 and

32 235 65 100 50 95-120 25 67 110 18 55 35-42 5

50 220 60 115 50 55 (125) end 65 115 28 55 45

nil 1 nil 1-2 1-2 1 nil nil nil nil nil 4

40-55 peak 48 45-55 small peaks

all

200 32 235 55 98 50 130 35 65 110 18 55 33

nil nil nil nil nil 1 nil nil nil nil nil nil 4

peak 45

all

Other origin 204 (IC), 268 (CA), 279(LE), 336, 341, 359 (Oman)

Cut Off 25 x x

Chrom

Ind. freq

3 3 3 7 7 9 10 11 11 15 16 21 X

1-3 1-3 1-2 1-2 4 1-3 1-4 1-4 4 1-3 1-2 2-4 1-5

STY Dist. telomer (Mb) start stop 30 115 185 7

peak at 30 29

70 125 190 22 130 0 22 45 123 70 peak at 75 peak at 48 43

Ind. freq

control start-stop

1-3 nil 1 nil 135 1-2 12 nil 25 1 70 1-2 124 nil 1-2; nil at 75 1-4 1-2 3-5

40-50

1 130 nil nil nil 135 1 10 nil nil nil 70 1-2 nil nil nil 33 nil 3

peak 60

185 130

45-55 70 peaks at 30, 48 peaks at 29, 36 etc all

NSP Dist. telomer (Mb) start stop

Chrom

Ind. freq

3 3 3 7 7 9 10 11 11 15 16 21 X

1-3 1-3 1-2 1-3 4 1-3 1-4 1-4 4 1-4 1-2 1-4 2-5

30 100 185 7 130 0 20 45 123 70 30 25

75 135 195 48 135 12 23 70 124 peak at 75 48 43

3 3 3 7 7 9 10 10 11 11 15 16 21 X

1-2 1-3 1-2 1-2 1-4 1-3 1-2 1-2 1-4 1 1 1 1-3 1-5

30 100 185 5 128 0 5 85 35 95 35 30 25

73 133 190 45 150 12 30 110 70 125 80 48 43

3 3 3 7 7 9 10 11 11 15 16 21 X

1 1-3 1 1-2 1 1-2 1 1 1 1 nil 1-2 1-3

50 x x

3 3 3 7 7 9 10 10 11 11 15 16 21 X

1

25 1-3 1-2 1-2 1-4 2-3 2 2 1-3 1 1-2 1 1-2 2-4

70 100

185 10 130

190 23 5

25 85

30 95 45

95 70 peak at 48

125 75 25

133

45-57

all

200 3 3 3 7 7 9 10 11 11 15 16 21 X

nil 1 1 1 1 1 1 nil 1 1 nil 1-2 1-3

25 125 185 30 135

70 190 35 145 5

45 85 94 70 35 5

50 95 45 55 98 75 42 160

nil 130 nil nil nil nil 10 nil nil nil 1 nil nil nil 3

47-50

all

33 105 185 5 130 5 95 55 35 70 35 5

66 135 190 20 (45) 150 5 25 (80) 110 120 60 65 75 42 150

All 025, 039, 146, 153, 156, 186, 204, 268, 279, 252, 332, 336, 341, 350, 359 STY Dist. telomer (Mb) Cut Off Chrom Ind. freq start stop 25 50

Ind. freq

control start-stop

Chrom

Ind. freq

NSP Dist. telomer (Mb) start stop

Ind. freq 4 peaks, peak 52 peaks, no peak 80 nil

control start-stop peak 210

no peak 30, peaks 25, 40 peaks peak 57 small peaks peak 10,12, 22 peak 47,55 peaks 28, 30, 40 5-9

all

nil peak 50 peak 40 nil peaks 25, 35 peaks small peak 57 a nil nil peak s 28, 30 5-6

all

nil nil nil nil nil nil nil nil nil nil nil nil all

Known Disease Loci

Ind. freq

control start-stop

1-2 1-3 1 1-4 2 1 1 1-4 1 1 1 1-3 3-6

peaks peaks 190 peaks 133 peak at7

1 nil nil nil 1 nil 1 2 1-3 nil nil nil 1 3-4

some peaks

nil nil nil nil nil nil 1 1 nil nil nil nil 3

peaks at 47, 57 peak at 123 peak peak at 48 peaks at 30, 40 all

peak at 145 peaks 17, 25 peak 105 peaka at 38, 55

peaks at 28, 30 5-150

35-45 peak 90

all

exons 4 7 33

gene Unknown PRF1 UNC13D STX11 MYHIIA

chromosome 6 9

cytoband 6q24 9q21.3-22

10 17 22

10q21-22 17q24 22q12.3

protein expression disease status Unknown FHL1 Perforin FHL2 Munc 13-4 FHL3 Syntaxin 11 FHL4 Myosin ?

Distance from telomer (Mb) start stop length (Mb) length (SNPs) ca 142 ca 149 ca 7 ca 71 ca 60 ca 31

chromosome 9 10 17 6 22

ca 81 ca 65 ca 38

cytoband 9q21.3-22 10q21-22 17q24 6q24 22q12.3

ca 10 ca 5 ca 7

exons 7 33 4

Ind. freq

control start-stop

genes protein expression disease status STX11 Syntaxin Syntaxin 11 FHL4 Unknown Unknown FHL1 PRF1 Perforin UNC13D MYHIIA

Perforin Munc 13-4 Myosin

FHL2 FHL3 ?

Individual Analysis Individual to investigate (CO 50) 25 Gender M Chromosome STY NSP 1x x 2 3 3: 100-130 4 5 6 7 8x x 9 10 11 12 12: 52-65 (Nsp) 12: 45-55 13 14 15 16 17 18 19 20 21 22 X C

STY x x x

39 M NSP x x x

146 F STY NSP x

x x

x

x x x

x x x

x

x

x x

x

x x

x x

186 F STY NSP

252 M STY NSP

x

x

x

x x x x

x x

x x

x

x x x x

x

x x x

x

x

C

350 M STY NSP x x

x

x

204 ? STY NSP

x x

x x

x x x x x x x

x x x x x x x x x

x x x x x x x x

x x x x x x x x

x

x

x x

268 ? STY NSP

x

x x

x

x

x

x

x

x

279 F STY NSP

Other STY

x

x

x

x

0x C

332 M STY NSP x x x x x x

x x

x

x x

153 F STY NSP

Turkish 156 F STY NSP x x

x x

x x x

x x x x

x

x

x

x

x

x

x

x x

x

x

x

x

336 M

36 M NSP

341 M STY NSP x x

x x x x x

359 ? STY NSP x x x

x x

x x x x

x x

x x

x x

x

x x

x

x x

x x

x x

x x

x

x

x

x

x

x

x

x

Individual Gene Analysis

Gene Characteristics Chromosome Gene

Cytoband

Region (Mb)

Protein

Subcellular location

3p21.31

45.903023-45.919671

C-C chemokineMembrane; receptor type multi-pass 9 (C-C CKRmem FYVE and coiled-coil domain-containing p C-X-C chemokine Membrane; receptormulti-pass type 6 (CXC-R6 mem

1 2 3 CCR9 FYCO1

45.934400-46.012304

CXCR6

45.959977-45.964849

PCNP

102.775732-102.795971

ALCAM BBX CD47 PVRL3 CD96

PEST-containing nuclear protein ALCAM protein (Activated leukocyte cell a HMG-BOX transcription factor BBX CD47 antigen isoform 1 precursor nectin 3 CD96 antigen isoform 2 precursor

DRD3

CD200

113534606-113564348

CDNA FLJ31797 fis, clone NT2RI2008942 growth associated protein 43 limbic system-associated membrane prot immunoglobulin (Ig) superfamily member uroplakin 1B G protein-coupled receptor 156 DNA polymerase theta CD200 antigen isoform b

CD200R1

114124222-114176627

CD200 receptor 1 isoform a

CD80

120725830-120761171

CD80 antigen precursor CD86 antigen isoform 1

123623438-123662194

karyopherin alpha 1

BCL6

188921859-188936942

cystatin A adenylate cyclase 5 B-cell lymphoma 6 protein (BCL-6) (Zinc f

FLJ21903

46.343341-46.386041

hypothetical protein LOC79657 NK, B, T, monocytes, dendritic, lymph

P11

46.389795-46405617

AL831948

46.399301-46.422344

RAPGEF3

46.417293-46.422342

placental protein 11 precursor Homo sapiens mRNA; cDNA DKFZp761B0 RAP guanine-nucleotide-exchange factor

BOC GAP43 LSAMP IGSF11

q23.1

120102169-120236366

UPK1B GPR156 POLQ

CD86 KPNA1 CSTA ADCY5 4 5 6 7 8 9 10 11 12

FLJ20489

46.451637-46.462801

HDAC7A

46.462774-46.473638

VDR

46.521587-46.5850

TMEM106C

46.643634-46.648928

COL2A1

46.653015-46.655663

SENP1

46.723024-46.785908

PFKM

46.785973-46.826154

ASB8

46.827839-46.837644

LOC387856

46.863666-46.865976

DKFZp779L1853

46.878411-46.882113

OR10AD1

46.882389-46.883342

H1FNT

47.009030-47.010329

ZNF641

47.022179-47030268

AX747699

47.030111-47.030843

ANP32D

47.152715-47.153110

Homo sapiens cDNA FLJ20489 fis, clone K histone deacetylase 7A isoform b Homo sapiens vitamin D receptor (VDR) m hypothetical protein LOC79022 Collagen alpha-1(II) chain precursor [Con Protease that catalyzes Nucleus. Cytoplasm. two essential Note= fun Phosphofructokinase (EC 2.7.1.11) (PFKM ankyrin repeat and SOCS box-containing hypothetical protein LOC387856 Hypothetical protein DKFZp779L1853. olfactory receptor, family 10, subfamily A histone H1 variant zinc finger protein 641 Homo sapiens cDNA FLJ35421 fis, clone S acidic nuclear phosphoprotein 32D

47.163290-47.176434

hypothetical protein LOC121273

OR8S1 LALBA C12orf54 DKFZp762L0110 C120rf41 NR_002968 NR_002950 NR_002951 BX537516

BIN2 ELA1 GALNT6 krt5 hoxc12 or6c6 ITGA7 EIF4B CBX5 CD63 GDF11

13

54364621-54387894 51686490-51722260 52921677-52939585 CD63 antigen isoform A

14 15 16 CD19 STX4

p11.2

28850761-28858164

LAT

p11.2

30951917-30958586

MLAS

p11.2

28903027-28909605

CD19 antigen Homo sapiens syntaxin 4 (STX4) mRNA, c linker for activation of T cells isoform c

29531925-29532539

HLAT1-3TM

45746799-46052516

T-cell immunomodulatory protein (TIP pro Genes encoding immunoglobulin heavy c

146,9-154,9

synaptobrevin-like 1

ITFG1 IGHV IGHV3-30

q21

IGH

q21 q21

18 19 20 21 22 SYB1 (VAMP7) X

q28

thymocytes recruitment and development that may permit functional specialization 25 39 146 of immune STY NSP STY NSP STY responses in Tissue Function different segment of the gastrointesti Highly expressed nal tract. in the thymus and low in lymph nodes and spleen. Expressed in heart and skeletal muscle. Expressed in lymphoid Receptor tissues for the and C-X-C activated chemokine T cells. CXCL16. Used as a coreceptor by SIVs and by strains

PESTdentritic proteolytic signal-containing nuclear protein. Maylymphoblasts be involved BM CD-cells, PB CD-cells, cells, NK-cells, monocytes, T-cells, B-cells, several leukemia

in cell cycle regulati

epithelal cells, brain, dendritic cells B-cells

orm 1 precursor

Receptor for PTPNS1. May play a role in membrane transport and/or signal transduction Nectins (e.g., PVRL1; MIM 600644) are immunoglobulin-like adhesion molecules that int immunoglobulin superfamily. It is a type I membrane protein. The protein may play a ro NK-cells, CD4-and CD8 T-cells

, clone NT2RI2008942 CDON (MIM 608707) and BOC are cell surface receptors of the immunoglobulin (Ig)/fibro This protein is associated with nerve growth. It is a major component of the motile "grow brain ociated membrane protein. Mediates Belongs selective to the immunoglobulin neuronal growthsuperfamily. and axon targeting. IgLON faContributes to the guidance of brain, testis

Component of the asymmetric unit membrane (AUM); a highly specialized biomembrane CNS and in peripheral Orphan receptor tissues BM CD34, different leukemia lymphoblasts

belongs to the immunoglobulin superfamily. Studies of the related genes in mouse and

encodes a receptor for the OX-2 membrane glycoprotein. Both the receptor and substrate are cell surf Involved in the costimulatory signal essential for Expressed on activated B-cells, macrophages and dendritic cells. pancreas, liver etc

T- lymphocyte activation. T-cell prolifer This gene protein that is a member of the immunoglobulin superfamil encodes a Recombination protein with activating proteins RAG1 and RAG2 regulate and mediate V(D)J recombination, the encodes blood, lymph system protease a stefin that functions as a cysteine protease inhibitor, forming tight complexes activity. Its protein (BCL-6) (Zinc finger Transcriptional protein 51)regulator (LAZ-3 protein) that probably (BCL-5)plays (Zincan finger important and BTB role domain-containing in lymphomagenesis. protein Th specific function has not been determined. The protein may be useful as a tumor marker; Probable serine whole blood etc protease. Placental specific, but also associated with various malignant neoplasms NA; cDNA DKFZp761B0218 (from clone DKFZp761B0218). otide-exchange factor 3 encodes a type I membrane NK-cells, T-cells, B-cells, dendtritic cells, monocytes

A FLJ20489 fis, clone KAT08285. e 7A isoform b min D receptor (VDR) mRNA, This gene complete encodes cds.the nuclear hormone receptor for vitamin D3. This receptor also func n LOC79022 ) chain precursor [Contains: This gene Chondrocalcin]. encodes the alpha-1 chain of type II collagen, a fibrillar collagen found in cart Highly expressed in testis. Expressed at lower levels in thymus, pancreas, spleen, liver, ovary and sma se (EC 2.7.1.11) (PFKM protein). d SOCS box-containing 8 n LOC387856 in DKFZp779L1853. family 10, subfamily AD): Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal

A FLJ35421 fis, clone SMINT2001195, weakly similar to ZINC FINGER PROTEIN 202. sphoprotein 32D Phosphoprotein 32 (PP32) is a tumor suppressor that can inhibit several types of cancer

n LOC121273

NK- cell, T-cells, B-cells

n of T cells isoform c

protein encoded by this gene is phosphorylated by ZAP-70/Syk protein tyrosine kinases

, dendritic, macrophages Lymphocytes proliferate and differentiate in response to various concentrations of differ

Individual to invest Turkish 146 NSP

153 STY

NSP

156 STY

NSP

186 STY

NSP

or by SIVs and by strains of HIV-2 and m-tropic HIV-1.

ved in cell cycle regulation

nd/or signal transduction. May prevent premature elimination of red blood cells. May be involved in membrane p esion molecules that interact with afadin (AF6; MIM 159559). he protein may play a role in the adhesive interactions of activated T and NK cells during the late phase of the i

mmunoglobulin (Ig)/fibronectin type III (FNIII; see MIM 135600) repeat family involved in myogenic differentiatio onent of the motile "growth cones" that form the tips of elongating axons. butes to the guidance of developing axons and remodeling of mature circuits in the limbic system. Essential for

specialized biomembrane elaborated by terminally differentiated urothelial cells. May play an important role in n

ted genes in mouse and rat suggest that this gene may regulate myeloid cell activity and delivers an inhibitory

or and substrate are cell surface glycoproteins containing two immunoglobulin-like domains. This receptor is restricted to the su

activation. T-cell proliferation and cytokine production is induced by the binding of CD28 or CTLA-4 to this rece munoglobulin superfamily. This protein is expressed by antigen-presenting cells, and it is the ligand for two prot

e V(D)J recombination, the process by which genes for immunoglobulins and T-cell receptors are generated. forming tight complexes with papain and the cathepsins B, H, and L

in lymphomagenesis. This protein acts as a sequence-specific repressor of transcription, and has been shown to

3. This receptor also functions as a receptor for the secondary bile acid lithocholic acid. The receptor belongs to

ar collagen found in cartilage and the vitreous humor of the eye. Mutations in this gene are associated with ach een, liver, ovary and small intestine

se, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are m

t several types of cancers, including prostate and breast cancers. The protein encoded by this gene is one of at

protein tyrosine kinases following activation of the T-cell antigen receptor (TCR) signal transduction pathway. T

s concentrations of different antigens. The ability of the B cell to respond in a specific, yet sensitive manner to t

x

x

Individual to investigate 252 STY

332 NSP

STY

NSP

350 STY

NSP

204 STY

y be involved in membrane permeability changes induced following virus infection. May play a role in memory

during the late phase of the immune response. It may also function in antigen presentation.

ved in myogenic differentiation limbic system. Essential for normal growth of the hyppocampal mossy fiber projection (By similarity).

ay play an important role in normal bladder epithelial physiology, possibly in regulating membrane permeability

ty and delivers an inhibitory signal for the macrophage lineage in diverse tissues.

his receptor is restricted to the surfaces of myeloid lineage cells and the receptor-substrate interaction may function as a myeloid

f CD28 or CTLA-4 to this receptor; The B-lymphocyte activation antigen B7-1 (formerly referred to as B7) pr ovid nd it is the ligand for two proteins at the cell surface of T cells, CD28 antigen and cytotoxic T-lymphocyte-assoc

are generated.

ption, and has been shown to modulate the transcription of START-dependent IL-4 responses of B cells.

acid. The receptor belongs to the family of trans-acting transcriptional regulatory factors and shows sequence s

gene are associated with achondrogenesis, chondrodysplasia, early onset familial osteoarthritis, SED conge nita

ctory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from sing le

ded by this gene is one of at least two proteins that are similar in amino acid sequence to PP32 and are part o f

gnal transduction pathway. This transmembrane protein localizes to lipid rafts and acts as a docking site for SH

fic, yet sensitive manner to the various antigens is achieved with the use of low-affinity antigen recepto rs. This

x

x

x

x

x

x

Other 204 NSP

268 STY

NSP

279 STY

NSP

336 STY

NSP

May play a role in memory forma tion. Has a role in cell adhesion

on (By similarity).

ng membrane permeability of superficial umbrella cells or in stabilizing the apical membrane through AUM/cyt

ion may function as a myeloid downregulatory signal.

y referred to as B7) pr ovides regulatory signals for T lymphocytes as a consequence of binding to the CD28 (M otoxic T-lymphocyte-assoc iated protein 4. Binding of this protein with CD28 antigen is a costimulatory signal fo

sponses of B cells.

ors and shows sequence similarity to the steroid and thyroid hormone receptors. Downstream targets of this nu

eoarthritis, SED conge nita, Langer-Saldino achondrogenesis, Kniest dysplasia, Stickler syndrome type I, and sp

(GPCR) arising from sing le coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure

ce to PP32 and are part o f the same acidic nuclear phosphoprotein gene family. However, unlike PP32, the enco

ts as a docking site for SH2 domain-containing proteins. Upon phosphorylation, this protein recruits multiple ad

nity antigen recepto rs. This gene encodes a cell surface molecule which assembles with the antigen receptor of

x

x

x

l membrane through AUM/cytoskeletal interactions (By similarity).

nce of binding to the CD28 (MIM 186760) and CTLA4 (MIM 123890) ligands of T cells.[ en is a costimulatory signal for activation of the T-cell. Binding of this protein with cytotoxic T-lymphocyte-assoc

Downstream targets of this nuclear hormone receptor are principally involved in mineral metabolism though th

ckler syndrome type I, and spondyloepimetaphyseal dysplasia Strudwick type. In addition, defects in processing

smembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the r

However, unlike PP32, the encoded protein is tumorigenic. The tumor suppressor function of PP32 has been loca

his protein recruits multiple adaptor proteins and downstream signaling molecules into multimolecular signaling

s with the antigen receptor of B lymphocytes in order to decrease the threshold for antigen receptor-dependen

cytotoxic T-lymphocyte-associated protein 4 negatively regulates T-cell activation and diminishes the immune

mineral metabolism though the receptor regulates a variety of other metabolic pathways, such as those involve

addition, defects in processing chondrocalcin, a calcium binding protein that is the C-propeptide of this collagen

s and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory

unction of PP32 has been localized to a 25 amino acid region that is absent in the protein encoded by this gene

s into multimolecular signaling complexes located near the site of TCR engagement.

or antigen receptor-dependent stimulation.

n and diminishes the immune res ponse.

thways, such as those involved in the immune response and cancer. Mutations in this gene are associated with

e C-propeptide of this collagen mol ecule, are also associated with chondrodysplasia.

odorant signals. The olfactory receptor gene family is the largest in the genome.

protein encoded by this gene. This gene does not contain introns.

this gene are associated with type II vitamin D-resistant rickets. A single nucleotide polymorphism in the initiat

de polymorphism in the initiation codon results in an alternate translation start site three codons downstream.

te three codons downstream. Alternative splicin g results in multiple transcript variants encoding the same prot

riants encoding the same protein.