Bio lab 13 - Lab report PDF

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BIOL203- SPRING 2020 LAB13 LAB REPORT—Total point value: 50pts LINK TO THE WIKIPAGE EXERCISE FOR LAB 13: http://diverge.hunter.cuny.edu/labwiki/QuBi/modules/biol203-geno-phenoassociation-2020 THE TWO DATA TABLES AND THE DNA SEQUENCE NEEDED FOR COMPLETION OF THE REPORT ARE EMBEDDED IN THE TEXT-SEE BELOW Introduction: GWAS and contingency test

T/T

T/C

C/C

Total

Case

0

24

127

151

Control

9

68

114

191

Total

9

92

241

342

chi-square = 26.4 degrees of freedom = 2 probability = 0.000 Tabl e2.Sampl eAl l el eFr equenci es T

C

Tot al

Case

24

278

302

Cont r ol

86

296

382

Tot al

110

574

684

Is there a statistically significant association between alleles and disease phenotype? As the chi-square value is 26.5, and the p value being less than 0.05, this means that there is a significant association between alleles and disease phenotype. In this case, the null hypothesis should be rejected. Which allele (C or T) is over-represented in (i.e., statistically associated with) disease cases? The C allele is over-represented, as seen from tables 2a and 2b.

Test Association with locus A TABLE 3a. Genotype counts at Locus A for each phenotype A1/A A1/A A2/A Row 1 2 2 Sum Taster 62 26 48 136 Non-Taster 18 15 56 89 Column 80 41 104 225 Sum Tabl e3b.Al l el ecount satLocusA A1

A2

Row Sum

Tast er

150

122

272

NonTast er

51

127

178

Col umnSum

201

249

450

Recor dyourr esul ti nt hel abr epor tsheetf ort hecont i ngencyt es tf orLocusA,i nc l udi ngchi s quar es t at i s t i c ,degr eeoff r eedom,andpv al ues

chi-square = 30.6 degrees of freedom = 1 probability = 0.000 expected: contingency table

1 2

A

B

121. 79.5

151. 98.5

Test Association with locus B TABLE 4a. Genotype counts at Locus B for each phenotype B1/B B1/B B1/B B2/B B2/B B3/B 1 2 3 2 3 3 Taster 16 9 8 51 4 1 Non-Taster 11 7 1 31 9 0 Column 27 16 9 82 13 1 Sum

Row Sum 89 59 148

B1 B2 B3 Ro wSum

Ta s t e r

49 11 5 14 17 8

No nTa s t e r

30 78

Col umnSum

79 19 3 24 29 6

10 11 8

Recor dy ourr esul ti nt hel abr epor tsheetf ort hecont i ngenc yt es tf orLocusA,i nc l udi ngchi s quar es t at i s t i c ,degr eeoff r eedom,andpv al ues

chi-square = 0.175 degrees of freedom = 2 probability = 0.916

Web Exercise. Search for gene information using NCBI online databases Past ey ourbl as thi tbel ow( y oumi ghtwantt ous et hepr i nt / pdff unc t i onori mpor ta phonepi c t ur e) :

Name of the gene and summary of its function (from locus page): This gene is named TAS2R38, and represents the taste 2 receptor member 38. This has a G-PCR, which controls our ability to taste glucosinolates.

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2.Ex pl ai nwhatpr obabi l i t yi sr epr es ent edbyt hepv al ue. Thepval uei st hepr obabi l i t yofwhet hert hedat ai sr el i abl eornot .Al ar gepv al ue s uppor t st henul l hypot hesi s .

3.Whatcany ouconcl udewhenpv al uei sbel ow t het hr eshol dofsi gni ficance( e. g. ,p= 0. 05) ? Whent hepv al uei sbel owp>0. 05,t hi smeanst hatt heexper i ment alfi ndi ngsar enot s i gni fic ant .

4.Whatwoul dy ouconc l udewhenpv al uei sabovet hec r i t i c alv al ue ? Whent hepv al uei sbel owp...