Screening analysis of candidate gene mutations in a kindred with polycystic liver disease

doi:10.3748/wjg.v21.i8.2343

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World Journal of Gastroenterology

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1007-9327

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Baishideng Publishing Group Inc, 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA

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World J Gastroenterol. Feb 28, 2015; 21(8): 2343-2351
Published online Feb 28, 2015. doi: 10.3748/wjg.v21.i8.2343

Table 1 Primers for amplification of PKD1 b long-range polymerase chain reaction

Fragment	Size (bp)	Exon	Forward primer	Reverse primer	Temperature(°C)
Exon 1	2278	1	5’-CGCAGCCTTACCATCCACCT-3’	5’-TCATCGCCCCTTCCTAAGCA-3’	64
Exons 2-7	4041	2-7	5’-CCCCGAGTAGCTGGAACTACAGTTACACACT-3’	5’-CGTCCTGCTGTGCCAGAGGCG-3’	70
Exons 8-12	3893	8-12	5’-ACGTCTGCGAGCTGCAGCCC-3’	5’-CTGCAGGGACAGGCGTCAGTGA-3’	70
Exons 13-15	4391	13-15	5’-TGGAGGGAGGGACGCCAATC-3’	5’-GTCAACGTGGGCCTCCAAGT-3’	65
Exons 15-21	5253	15-21	5’-ATCCCTGGGGGTCCTACCATCTCTTA-3’	5’-ACACAGGACAGAACGGCTGAGGCTA-3’	68
Exons 22-26	3276	22-26	5’-ATGCTTAGTGAGGAGGCTGTGGGGGTCCA-3’	5’-GCTTAAAGGGGAATGGCTTAAACCCG-3’	70
Exons 27-34	3916	27-34	5’-CGGGTCACCGGTTGTGGCA-3’	5’-ATGAGGCTCTTTCCACAGACAACAGAGGTT-3’	70
Exons 35-41	2632	35-41	5’-CAAGAGGCTCAAGAAACTGCCCG-3’	5’-GGGCTGTGGAAGCCGCCTA-3’	68
Exons 42-46	2370	42-46	5’-GAGTAGTTCTCCAGGAGTGCCG-3’	5’-ATTCTGCCTGGCCCTCGGCCTT-3’	63

Full Size Table

Table 2 Primers for sequencing of PKD1 exons

Primer name	Sequence	Genomic position (starting from the 5’ end)	Distance to exon-intron junction	Exons covered
PKD1-exon1-F	5’-GCGTCGCTCAGCAGCAGGT-3’	2185830	-140 Ex1	1
PKD1-exon1-R	5’-GCCCGCGTCCTGCTTCCC-3’	2185383	93 Ex1
PKD1-exon2-3-F	5’-GGGATGCTGGCAATGTGTGGGAT-3’	2169468	-89 Ex2	2-3
PKD1-exon2-3-R	5’-GGACCAACTGGGAGGGCAGAA-3’	2169038	77 Ex3
PKD1-exon4-F	5’-GGCGGTGCTGTCAGGGTG-3’	2168948	-102 Ex4	4
PKD1-exon4-R	5’-CCAGAGAGGCCTTCCTGAGC-3’	2168582	95 Ex4
PKD1-exon5A-F	5’-GAACAGCATGGGAGCCTGTGAGT-3’	2168561	-98 Ex5	5
PKD1-exon5A-R	5’-AGCCGGCCCAGCGGCATC-3’	2168033	Within an exon
PKD1-exon5B-F	5’-GCCTGTCCCTCTGCTCCG-3’	2168262	Within an exon	5
PKD1-exon5B-R	5’-GTGTCAACGGTCAGTGTGGGC-3’	2167696	96 Ex5
PKD1-exon6-F	5’-GTGTCTGCTGCCCACTCCC-3’	2167787	-124 Ex6	6
PKD1-exon6-R	5’-CTCCTTCCTCCTGAGACTCCC-3’	2167397	93 Ex6
PKD1-exon7-F	5’-GCTGCTGTGAGGGTGGGAGGA-3’	2167120	-66 Ex7	7
PKD1-exon7-R	5’-TCCACCGCGGGCGCTCGGCA-3’	2166763	71 Ex7
PKD1-exon8-F	5’-CTGGGCTGAGGAGGAGGG-3’	2166760	-115 Ex8	8
PKD1-exon8-R	5’-GGGCACAAGCAACATTAAGGCCC-3’	2166413	117 Ex8
PKD1-exon9-F	5’-CCTCTTCCTGGGAAGTTCGGGT-3’	2166206	-87 Ex9	9
PKD1-exon9-R	5’-ACTCTGGTGGCCACAGGACCA-3’	2165895	98 Ex9
PKD1-exon10-F	5’-GCAGGCAGTTGGGCATCTCTG-3’	2165697	-71 Ex10	10
PKD1-exon10-R	5’-GACCCTGGGCAGCAGACAG-3’	2165309	70 Ex10
PKD1-exon11A-F	5’-GTGTGGCTGACGAAGCGGG-3’	2165035	-109 Ex11	11
PKD1-exon11A-R	5’-CCGTGGCGTTGGCACCAG-3’	2164455	Within an exon
PKD1-exon11B-F	5’-CGCTATGAGGTCCGGGCAG-3’	2164641	Within an exon	11
PKD1-exon11B-R	5’-CCCTCACTGGGAAGCCAGG-3’	2164077	93 Ex11
PKD1-exon12-F	5’-GGACTCTCCAGCCCGACG-3’	2163387	-94 Ex12	12
PKD1-exon12-R	5’-GCAGAGGTGAAGGTGGAGC-3’	2163088	74 Ex12
PKD1-exon13-14-F	5’-GTGGAGGGAGGGACGCCAA-3’	2163037	-73 Ex13	13-14
PKD1-exon13-14-R	5’-GTCACAGTGAGGGCTGTTGGG-3’	2162230	111 Ex14
PKD1-exon15A-F	5’-TTCTGCCGAGCGGGTGGG-3’	2161938	-64 Ex15	15
PKD1-exon15A-R	5’-CATGTCGAAGGTCCACGTGATGT-3’	2161427	Within an exon
PKD1-exon15B-F	5’-GACATGAGCCTGGCCGTGG-3’	2161516	Within an exon	15
PKD1-exon15B-R	5’-CCACCTCTGGCTCCACGCA-3’	2161027	Within an exon
PKD1-exon15C-F	5’-CACGCGGAGCGGCACGTT-3’	2161121	Within an exon	15
PKD1-exon15C-R	5’-GGTGACCTCCGGACCCTC-3’	2160626	Within an exon
PKD1-exon15D-F	5’-TCTGCTGTGGGCCGTGGG-3’	2160706	Within an exon	15
PKD1-exon15D-R	5’-CTGTACCGTGTGGTTGGTGGG-3’	2160215	Within an exon
PKD1-exon15E-F	5’-ACAGCATCTTCGTCTATGTCCTG-3’	2160303	Within an exon	15
PKD1-exon15E-R	5’-GGTTCCCTGCCGTCATGGTG-3’	2159812	Within an exon
PKD1-exon15F-F	5’-GGGCTGAGCTGGGAGACCT-3’	2159899	Within an exon	15
PKD1-exon15F-R	5’-GACAGCTGAGCCGGCAGC-3’	2159417	Within an exon
PKD1-exon15G-F	5’-CTGTGGGCCAGCAGCAAGGT-3’	2159494	Within an exon	15
PKD1-exon15G-R	5’-CGTGCGGTTCTCACTGCCCA-3’	2159012	Within an exon
PKD1-exon15H-F	5’-GACGTCACCTACACGCCCG-3’	2159095	Within an exon	15
PKD1-exon15H-R	5’-CCTCCCAGCGGTACTCAGTCT-3’	2158603	Within an exon
PKD1-exon15I-F	5’-GATGCGGCGATCACAGCGCA-3’	2158688	Within an exon	15
PKD1-exon15I-R	5’-GGCCAGCCCTGGTGGCAA-3’	2158164	89 Ex15
PKD1-exon16-F	5’-GGCCCGTCCTCAGTGCCT-3’	2158167	-134 Ex16	16
PKD1-exon16-R	5’-GCGGCCTCCACCAGCACTA-3’	2157790	94 Ex16
PKD1-exon17-18-F	5’-GAAACCTGGAGTTTGGGAGCAGC-3’	2157047	-98 Ex17	17-18
PKD1-exon17-18-R	5’-TGACGTCACAGAGTCGGG-3’	2156344	55 Ex18
PKD1-exon19-20-F	5’-GCACGGGTGAGTGCAGGC-3’	2156404	-99 Ex19	19-20
PKD1-exon19-20-R	5’-CCGGGATGAGCCCTCTGCAA-3’	2155768	98 Ex20
PKD1-exon21-F	5’-AGTCGTGGGCATCTGCTGGC-3’	2155550	-75 Ex21	21
PKD1-exon21-R	5’-CAAGCTGCCCGTCTGCCCT-3’	2155240	83 Ex21
PKD1-exon22-F	5’-CAGGTGAGGACCCGTGTAGAGA-3’	2154725	-82 Ex22	22
PKD1-exon22-R	5’-GGGAGGAGGGAGGCAGAG-3’	2154431	68 Ex22
PKD1-exon23A-F	5’-GCACCTCGCTCTCTGCCC-3’	2154024	-128 Ex23	23
PKD1-exon23A-R	5’-GCCACCTTGGTGGAGACGG-3’	2153512	Within an exon
PKD1-exon23B-F	5’-GGCTGCCACTTCTCCATCCC-3’	2153651	Within an exon	23
PKD1-exon23B-R	5’-GACACCCATGGAAGCCCTACG-3’	2153183	84 Ex23
PKD1-exon24-F	5’-CGTGGCAGAGGGTGGGCT-3’	2153064	-93 Ex24	24
PKD1-exon24-R	5’-CTCGCTGCCTGCCGTCCC-3’	2152721	94 Ex24
PKD1-exon25-26-F	5’-GGCTCTGAGACTGCGACATCCAA-3’	2152702	-68 Ex25	25-26
PKD1-exon25-26-R	5’-CTTGTTCTGACGCCTGCGACG-3’	2151964	98 Ex26
PKD1-exon27-28-F	5’-GCTGAGATGACTTGCCTGGGATG-3’	2150644	-77 Ex27	27-28
PKD1-exon27-28-R	5’-ACTGCAGGAGGCCACGGG-3’	2150094	73 Ex28
PKD1-exon29-30-F	5’-CTCCGTGGGAGGTTGGGCA-3’	2150142	-70 Ex29	29-30
PKD1-exon29-30-R	5’-CGCCTTTCCCTCTGGCTGC-3’	2149542	103 Ex30
PKD1-exon31-32F	5’-CGGGCTCTGTCCTGTCTGC-3’	2148079	-94 Ex31	31-32
PKD1-exon31-32R	5’-CCCAGCAAGGACACGCAGC-3’	2147642	87 Ex32
PKD1-exon33-34-F	5’-GGAAGCCCAGGGTGTCCGT-3’	2147595	-91 Ex33	33-34
PKD1-exon33-34-R	5’-CAGCCCTGCCCTGGCACC-3’	2147034	115 Ex34
PKD1-exon35-F	5’-CAAGAGGCTCAAGAAACTGCCCG-3’	2144309	-98 Ex35	35-36
PKD1-exon36-R	5’-GAGAAGTACAGGGCTTCCAGCAA-3’	2143714	98 Ex36
PKD1-exon37-F	5’-CTCGGCTGGGAGCCACTG-3’	2143832	-93 Ex37	37
PKD1-exon37-R	5’-GCCTTCTGAGGTGAGGAAAGGG-3’	2143439	106 Ex37
PKD1-exon38-F	5’-CCACACCTGCCGCAGCCAT-3’	2143190	-96 Ex38	38
PKD1-exon38-R	5’-CAAAGGTATCTACACATGTCCAC-3’	2142856	99 Ex38
PKD1-exon39-F	5’-GCCAGCAGGGCAGTGGGA-3’	2142698	-105 Ex39	39
PKD1-exon39-R	5’-CAGCTAGGGAGCAGGGCTGA-3’	2142385	96 Ex39
PKD1-exon40-F	5’-GTGGCGCCGAACCAGAGC-3’	2142289	-100 Ex40	40-41
PKD1-exon41-R	5’-GGGCTGTGGAAGCCGCCTA-3’	2141678	104 Ex41
PKD1-exon42-F	5’-CCTCAGCCACGCCTGCACT-3’	2141678	-80 Ex42	42
PKD1-exon42-R	5’-GGGTGAGACGCTGCCGGG-3’	2141338	86 Ex42
PKD1-exon43-F	5’-CAGCGTCCCTCCCGCCCT-3’	2141213	-38 Ex43	43-44
PKD1-exon44-R	5’-CAGGAAGACACGAGCTGCGG-3’	2140578	97 Ex44
PKD1-exon45-F	5’-GCTGGCCATCCTGGTAGGTGA-3’	2140687	-96 Ex45	45
PKD1-exon45-R	5’-GGACTTTGTGGCGGAACTGGG-3’	2140180	106 Ex45
PKD1-exon46-F	5’-GGAGAGGGACACGCCCTG-3’	2140264	-69 Ex46	46
PKD1-exon46-R	5’-ATTCTGCCTGGCCCTCGGCCTT-3’	2139635	Within 3’UTR

The genomic primer positions were according to the February 2009 human reference sequence (GRCh37/hg19). Ex: Exon; F: Forward; R: Reverse; UTR: Untranslated region.

Full Size Table

Table 3 Polymerase chain reaction reaction system setup

Polymerase chain reaction reaction system	Volume (μL)
LongAmp^® Taq DNA polymerase	1
LongAmp Taq reaction buffer	5
Deoxynucleotide solution mix	3
Dimethyl sulfoxide	1.25
Forward primer (10 μmol/L)	1
Reverse primer (10 μmol/L)	1
DNA template	1
H₂O	11.75
Total volume	25

Full Size Table

Citation: Jin S, Cui K, Sun ZQ, Shen YY, Li P, Wang ZD, Li FF, Gong KN, Li S. Screening analysis of candidate gene mutations in a kindred with polycystic liver disease. World J Gastroenterol 2015; 21(8): 2343-2351
URL: https://www.wjgnet.com/1007-9327/full/v21/i8/2343.htm
DOI: https://dx.doi.org/10.3748/wjg.v21.i8.2343

Jin S, Cui K, Sun ZQ, Shen YY, Li P, Wang ZD, Li FF, Gong KN, Li S. Screening analysis of candidate gene mutations in a kindred with polycystic liver disease. World J Gastroenterol 2015; 21(8): 2343-2351 [PMID: 25741140 DOI: 10.3748/wjg.v21.i8.2343]

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