Additional file 2: of Identification of mutations in the PI3K-AKT-mTOR signalling pathway in patients with macrocephaly and developmental delay and/or autism

Kit Yeung (4709332)
Winnie Tso (2816830)
Janice Ip (4709338)
Christopher Mak (4176853)
Gordon Leung (4176850)
Mandy Tsang (4709341)
Dingge Ying (367133)
Steven Pei (4709329)
So Lee (3777079)
Wanling Yang (50598)
Brian Chung (4709335)

Publication date

December 2017

DOI

10.6084/m9.figshare.5726605.v1

Abstract

Bi-allelic PTEN mutations in patient 3. The file consists of WES reads and clonal sequencing data to show that patient 3 has two mutations in different PTEN alleles. (DOCX 936Â kb

Extracted data

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Data Protection

Additional file 2: of Identification of mutations in the PI3K-AKT-mTOR signalling pathway in patients with macrocephaly and developmental delay and/or autism

Kit Yeung (4709332)
Winnie Tso (2816830)
Janice Ip (4709338)
Christopher Mak (4176853)
Gordon Leung (4176850)
Mandy Tsang (4709341)
Dingge Ying (367133)
Steven Pei (4709329)
So Lee (3777079)
Wanling Yang (50598)
Brian Chung (4709335)

Open link

Publication date

December 2017

DOI

10.6084/m9.figshare.5726605.v1

Abstract

Bi-allelic PTEN mutations in patient 3. The file consists of WES reads and clonal sequencing data to show that patient 3 has two mutations in different PTEN alleles. (DOCX 936Â kb

Extracted data

Angelica Bianco (1461580)
Luigi Bisceglia (13266)
Maria De Caro (5567237)
Valeria Galeandro (5567240)
Patrizia De Bonis (5567243)
Apollonia Tullo (62037)
Stefano Zoccolella (313665)
Silvana Guerriero (5567246)
Vittoria Petruzzella (5567249)

July 2018

Prioritization of mtDNA variants by MToolBox in LHON proband. All potentially deleterious mutations ...

Additional file 2: of Batten disease: biochemical and molecular characterization revealing novel PPT1 and TPP1 gene mutations in Indian patients

Jayesh Sheth (318977)
Mehul Mistri (318964)
Riddhi Bhavsar (5211767)
Dhairya Pancholi (5211761)
Mahesh Kamate (6080429)
Neerja Gupta (53651)
Madhulika Kabra (53650)
Sanjiv Mehta (6080432)
Sheela Nampoothiri (5229311)
Arpita Thakker (6080435)
Vivek Jain (310927)
Raju Shah (4535845)
Frenny Sheth (318968)

December 2018

In silico analysis of the functional effect of the variants identified in the patients with NCL1 and...

Additional file 1: Figure S1. of Novel MASP1 mutations are associated with an expanded phenotype in 3MC1 syndrome

Tahir Atik (824928)
Asuman Koparir (3435422)
Guney Bademci (222766)
Joseph Foster (3435410)
Umut Altunoglu (3435401)
GĂźl Mutlu (3435425)
Sarah Bowdin (524929)
Nursel Elcioglu (214959)
Gulsen Tayfun (3435404)
Sevinc Atik (3435416)
Mustafa Ozen (589386)
Ferda Ozkinay (214965)
Yasemin Alanay (3435407)
Hulya Kayserili (3435413)
Steffen Thiel (12664)
Mustafa Tekin (114701)

September 2015

Pedigrees of the studied families. Figure S2. Electropherograms showing detected pathogenic variants...

Additional file 3: of Mutations in RAB39B in individuals with intellectual disability, autism spectrum disorder, and macrocephaly

Marc Woodbury-Smith (4583911)
Eric Deneault (4583908)
Ryan Yuen (4583902)
Susan Walker (469919)
Mehdi Zarrei (3431519)
Giovanna Pellecchia (345990)
Jennifer Howe (625602)
Ny Hoang (4583899)
Mohammed Uddin (192247)
Christian Marshall (137748)
Christina Chrysler (4583914)
Ann Thompson (4583905)
Peter Szatmari (364570)
Stephen Scherer (3431540)

November 2017

RAB39B4_vs_Controls6_RPKM_Filt.txt (differential expression analysis results) (TXT 4721 kb

Additional file 3: of Inherited and multiple de novo mutations in autism/developmental delay risk genes suggest a multifactorial model

Hui Guo (110581)
Tianyun Wang (2884355)
Huidan Wu (6084857)
Min Long (397430)
Bradley Coe (6084860)
Honghui Li (383749)
Guanglei Xun (4776639)
Jianjun Ou (703720)
Biyuan Chen (6084863)
Guiqin Duan (6084866)
Ting Bai (92170)
Ningxia Zhao (6084869)
Yidong Shen (172967)
Yun Li (692280)
Yazhe Wang (1742299)
Yu Zhang (12946)
Carl Baker (196947)
Yanling Liu (218474)
Nan Pang (5181971)
Lian Huang (1889359)
Lin Han (113452)
Xiangbin Jia (6084872)
Cenying Liu (6084875)
Hailun Ni (6084878)
Xinyi Yang (324560)
Lu Xia (1509745)
Jingjing Chen (293564)
Lu Shen (161789)
Ying Li (38224)
Rongjuan Zhao (6084881)
Wenjing Zhao (318619)
Jing Peng (102796)
Qian Pan (77107)
Zhigao Long (3623711)
Wei Su (89824)
Jieqiong Tan (180436)
Xiaogang Du (745028)
Xiaoyan Ke (303580)
Meiling Yao (160516)
Zhengmao Hu (490757)
Xiaobing Zou (5454998)
Jingping Zhao (151214)
Raphael Bernier (196963)
Evan Eichler (3629480)
Kun Xia (9853)

December 2018

Figure S2. QC of MIPs cohort. QC analysis of the percentage of MIPs with at least eight reads per sa...

Additional file 2: of Delineation of the genetic and clinical spectrum of Phelan-McDermid syndrome caused by SHANK3 point mutations

Silvia De Rubeis (446496)
Paige Siper (4533643)
Allison Durkin (4533637)
Jordana Weissman (5148272)
FranĂ§ois Muratet (4533646)
Danielle Halpern (5148275)
Maria Trelles (5148266)
Yitzchak Frank (4533634)
Reymundo Lozano (4533649)
A. Wang (810509)
J. Holder (5148269)
Catalina Betancur (184790)
Joseph Buxbaum (3464495)
Alexander Kolevzon (3204279)

April 2018

Table S5. Descriptive and diagnostic data by patient. Table S6. ASD and intellectual ability classif...

Additional file 1: of Novel and de novo mutations in pediatric refractory epilepsy

Jing Liu (38537)
Lili Tong (1781044)
Shuangshuang Song (5722589)
Yue Niu (5538038)
Jun Li (6494)
Xiu Wu (721033)
Jie Zhang (64655)
Clement Zai (5809022)
Fang Luo (277928)
Jian Wu (41301)
Haiyin Li (450445)
Albert Wong (365470)
Ruopeng Sun (549506)
Fang Liu (13271)
Baomin Li (12997)

September 2018

Table S1. The expression levels of the 153 targeted genes in brain. Table S2. The quality assurance ...

Additional file 1: of Missense mutation in SLIT2 associated with congenital myopia, anisometropia, connective tissue abnormalities, and obesity

Katherine Liu (172225)
Jesse Sengillo (5636351)
Gabriel Velez (459875)
Ruben Jauregui (5636354)
Lynn Sakai (5636357)
Irene Maumenee (5636360)
Alexander Bassuk (5636363)
Vinit Mahajan (5636366)
Stephen Tsang (5636369)

August 2018

Table S1. BMI observations for proband and brother. Table S2. SLIT2 candidate gene. Table S3. SLIT2 ...

Additional file 2: of Identification of sequence variants associated with severe microtia-astresia by targeted sequencing

Pu Wang (171923)
Yibei Wang (5321825)
Xinmiao Fan (6271841)
Yaping Liu (165967)
Yue Fan (2227339)
Tao Liu (10785)
Chongjian Chen (6271844)
Shuyang Zhang (482315)
Xiaowei Chen (200607)

January 2019

Rare or novel mutations identified in severe microtia-astresia patients. Rare mutations were filtere...

Additional file 1: of Batten disease: biochemical and molecular characterization revealing novel PPT1 and TPP1 gene mutations in Indian patients

Jayesh Sheth (318977)
Mehul Mistri (318964)
Riddhi Bhavsar (5211767)
Dhairya Pancholi (5211761)
Mahesh Kamate (6080429)
Neerja Gupta (53651)
Madhulika Kabra (53650)
Sanjiv Mehta (6080432)
Sheela Nampoothiri (5229311)
Arpita Thakker (6080435)
Vivek Jain (310927)
Raju Shah (4535845)
Frenny Sheth (318968)

December 2018

List of primers used for PPT1 and TPP1 gene sequencing. The exons and the exon-intron boundaries of ...

Additional file 2: of Burden of de novo mutations and inherited rare single nucleotide variants in children with sensory processing dysfunction

Elysa Marco (5290844)
Anne Aitken (5290841)
Vishnu Nair (5290850)
Gilberto da Gente (5290859)
Molly Gerdes (5290856)
Leyla Bologlu (5290847)
Sean Thomas (75243)
Elliott Sherr (5290853)

May 2018

Moderate- Probability Risk ASD Gene Set. Table of 292 genes from AutDB categorized as possibly damag...

Additional file 2: of The altered activity of P53 signaling pathway by STK11 gene mutations and its cancer phenotype in Peutz-Jeghers syndrome

Yu-Liang Jiang (4595710)
Zi-Ye Zhao (4595716)
Bai-Rong Li (4595713)
Fu Yang (101882)
Jing Li (10611)
Xiao-Wei Jin (4595701)
Hao Wang (39217)
En-Da Yu (462877)
Shu-Han Sun (4595704)
Shou-Bin Ning (4595707)

August 2018

Figure S1. Flow diagram of patients enrollment. PJS indicates Peutz-Jeghers syndrome. Figue S2. The ...

Additional file 3: of Batten disease: biochemical and molecular characterization revealing novel PPT1 and TPP1 gene mutations in Indian patients

Jayesh Sheth (318977)
Mehul Mistri (318964)
Riddhi Bhavsar (5211767)
Dhairya Pancholi (5211761)
Mahesh Kamate (6080429)
Neerja Gupta (53651)
Madhulika Kabra (53650)
Sanjiv Mehta (6080432)
Sheela Nampoothiri (5229311)
Arpita Thakker (6080435)
Vivek Jain (310927)
Raju Shah (4535845)
Frenny Sheth (318968)

December 2018

ClinVar Accession ID of the novel variants generated in the given study. The variants identified thr...

Additional file 1: of The altered activity of P53 signaling pathway by STK11 gene mutations and its cancer phenotype in Peutz-Jeghers syndrome

Yu-Liang Jiang (4595710)
Zi-Ye Zhao (4595716)
Bai-Rong Li (4595713)
Fu Yang (101882)
Jing Li (10611)
Xiao-Wei Jin (4595701)
Hao Wang (39217)
En-Da Yu (462877)
Shu-Han Sun (4595704)
Shou-Bin Ning (4595707)

August 2018

Table S1. Primers for exon-specific sequencing of STK11 gene. Table S2. Native place of PJS patients...

Additional file 2: of PIK3CA activating mutations are associated with more disseminated disease at presentation and earlier recurrence in glioblastoma

Shota Tanaka (339198)
Tracy Batchelor (6648710)
A. Iafrate (6648713)
Dora Dias-Santagata (128565)
Darrell Borger (192022)
Leif Ellisen (6648716)
Daniel Yang (584075)
David Louis (6648725)
Daniel Cahill (5868119)
Andrew Chi (6648728)

April 2019

Figure S2. Kaplan-Meier curves of OS stratified by PIK3CA mutation. PIK3CA mutant tumors (solid) and...

Angelica Bianco (1461580)
Luigi Bisceglia (13266)
Maria De Caro (5567237)
Valeria Galeandro (5567240)
Patrizia De Bonis (5567243)
Apollonia Tullo (62037)
Stefano Zoccolella (313665)
Silvana Guerriero (5567246)
Vittoria Petruzzella (5567249)

July 2018

Prioritization of mtDNA variants by MToolBox in LHON proband. All potentially deleterious mutations ...

Additional file 2: of Batten disease: biochemical and molecular characterization revealing novel PPT1 and TPP1 gene mutations in Indian patients

Jayesh Sheth (318977)
Mehul Mistri (318964)
Riddhi Bhavsar (5211767)
Dhairya Pancholi (5211761)
Mahesh Kamate (6080429)
Neerja Gupta (53651)
Madhulika Kabra (53650)
Sanjiv Mehta (6080432)
Sheela Nampoothiri (5229311)
Arpita Thakker (6080435)
Vivek Jain (310927)
Raju Shah (4535845)
Frenny Sheth (318968)

December 2018

In silico analysis of the functional effect of the variants identified in the patients with NCL1 and...

Additional file 1: Figure S1. of Novel MASP1 mutations are associated with an expanded phenotype in 3MC1 syndrome

Tahir Atik (824928)
Asuman Koparir (3435422)
Guney Bademci (222766)
Joseph Foster (3435410)
Umut Altunoglu (3435401)
GĂźl Mutlu (3435425)
Sarah Bowdin (524929)
Nursel Elcioglu (214959)
Gulsen Tayfun (3435404)
Sevinc Atik (3435416)
Mustafa Ozen (589386)
Ferda Ozkinay (214965)
Yasemin Alanay (3435407)
Hulya Kayserili (3435413)
Steffen Thiel (12664)
Mustafa Tekin (114701)

September 2015

Pedigrees of the studied families. Figure S2. Electropherograms showing detected pathogenic variants...

Additional file 3: of Mutations in RAB39B in individuals with intellectual disability, autism spectrum disorder, and macrocephaly

Marc Woodbury-Smith (4583911)
Eric Deneault (4583908)
Ryan Yuen (4583902)
Susan Walker (469919)
Mehdi Zarrei (3431519)
Giovanna Pellecchia (345990)
Jennifer Howe (625602)
Ny Hoang (4583899)
Mohammed Uddin (192247)
Christian Marshall (137748)
Christina Chrysler (4583914)
Ann Thompson (4583905)
Peter Szatmari (364570)
Stephen Scherer (3431540)

November 2017

RAB39B4_vs_Controls6_RPKM_Filt.txt (differential expression analysis results) (TXT 4721 kb

Additional file 3: of Inherited and multiple de novo mutations in autism/developmental delay risk genes suggest a multifactorial model

Hui Guo (110581)
Tianyun Wang (2884355)
Huidan Wu (6084857)
Min Long (397430)
Bradley Coe (6084860)
Honghui Li (383749)
Guanglei Xun (4776639)
Jianjun Ou (703720)
Biyuan Chen (6084863)
Guiqin Duan (6084866)
Ting Bai (92170)
Ningxia Zhao (6084869)
Yidong Shen (172967)
Yun Li (692280)
Yazhe Wang (1742299)
Yu Zhang (12946)
Carl Baker (196947)
Yanling Liu (218474)
Nan Pang (5181971)
Lian Huang (1889359)
Lin Han (113452)
Xiangbin Jia (6084872)
Cenying Liu (6084875)
Hailun Ni (6084878)
Xinyi Yang (324560)
Lu Xia (1509745)
Jingjing Chen (293564)
Lu Shen (161789)
Ying Li (38224)
Rongjuan Zhao (6084881)
Wenjing Zhao (318619)
Jing Peng (102796)
Qian Pan (77107)
Zhigao Long (3623711)
Wei Su (89824)
Jieqiong Tan (180436)
Xiaogang Du (745028)
Xiaoyan Ke (303580)
Meiling Yao (160516)
Zhengmao Hu (490757)
Xiaobing Zou (5454998)
Jingping Zhao (151214)
Raphael Bernier (196963)
Evan Eichler (3629480)
Kun Xia (9853)

December 2018

Figure S2. QC of MIPs cohort. QC analysis of the percentage of MIPs with at least eight reads per sa...

Additional file 2: of Delineation of the genetic and clinical spectrum of Phelan-McDermid syndrome caused by SHANK3 point mutations

Silvia De Rubeis (446496)
Paige Siper (4533643)
Allison Durkin (4533637)
Jordana Weissman (5148272)
FranĂ§ois Muratet (4533646)
Danielle Halpern (5148275)
Maria Trelles (5148266)
Yitzchak Frank (4533634)
Reymundo Lozano (4533649)
A. Wang (810509)
J. Holder (5148269)
Catalina Betancur (184790)
Joseph Buxbaum (3464495)
Alexander Kolevzon (3204279)

April 2018

Table S5. Descriptive and diagnostic data by patient. Table S6. ASD and intellectual ability classif...

Additional file 1: of Novel and de novo mutations in pediatric refractory epilepsy

Jing Liu (38537)
Lili Tong (1781044)
Shuangshuang Song (5722589)
Yue Niu (5538038)
Jun Li (6494)
Xiu Wu (721033)
Jie Zhang (64655)
Clement Zai (5809022)
Fang Luo (277928)
Jian Wu (41301)
Haiyin Li (450445)
Albert Wong (365470)
Ruopeng Sun (549506)
Fang Liu (13271)
Baomin Li (12997)

September 2018

Table S1. The expression levels of the 153 targeted genes in brain. Table S2. The quality assurance ...

Additional file 1: of Missense mutation in SLIT2 associated with congenital myopia, anisometropia, connective tissue abnormalities, and obesity

Katherine Liu (172225)
Jesse Sengillo (5636351)
Gabriel Velez (459875)
Ruben Jauregui (5636354)
Lynn Sakai (5636357)
Irene Maumenee (5636360)
Alexander Bassuk (5636363)
Vinit Mahajan (5636366)
Stephen Tsang (5636369)

August 2018

Table S1. BMI observations for proband and brother. Table S2. SLIT2 candidate gene. Table S3. SLIT2 ...

Additional file 2: of Identification of sequence variants associated with severe microtia-astresia by targeted sequencing

Pu Wang (171923)
Yibei Wang (5321825)
Xinmiao Fan (6271841)
Yaping Liu (165967)
Yue Fan (2227339)
Tao Liu (10785)
Chongjian Chen (6271844)
Shuyang Zhang (482315)
Xiaowei Chen (200607)

January 2019

Rare or novel mutations identified in severe microtia-astresia patients. Rare mutations were filtere...

Additional file 1: of Batten disease: biochemical and molecular characterization revealing novel PPT1 and TPP1 gene mutations in Indian patients

Jayesh Sheth (318977)
Mehul Mistri (318964)
Riddhi Bhavsar (5211767)
Dhairya Pancholi (5211761)
Mahesh Kamate (6080429)
Neerja Gupta (53651)
Madhulika Kabra (53650)
Sanjiv Mehta (6080432)
Sheela Nampoothiri (5229311)
Arpita Thakker (6080435)
Vivek Jain (310927)
Raju Shah (4535845)
Frenny Sheth (318968)

December 2018

List of primers used for PPT1 and TPP1 gene sequencing. The exons and the exon-intron boundaries of ...

Additional file 2: of Burden of de novo mutations and inherited rare single nucleotide variants in children with sensory processing dysfunction

Elysa Marco (5290844)
Anne Aitken (5290841)
Vishnu Nair (5290850)
Gilberto da Gente (5290859)
Molly Gerdes (5290856)
Leyla Bologlu (5290847)
Sean Thomas (75243)
Elliott Sherr (5290853)

May 2018

Moderate- Probability Risk ASD Gene Set. Table of 292 genes from AutDB categorized as possibly damag...

Additional file 2: of The altered activity of P53 signaling pathway by STK11 gene mutations and its cancer phenotype in Peutz-Jeghers syndrome

Yu-Liang Jiang (4595710)
Zi-Ye Zhao (4595716)
Bai-Rong Li (4595713)
Fu Yang (101882)
Jing Li (10611)
Xiao-Wei Jin (4595701)
Hao Wang (39217)
En-Da Yu (462877)
Shu-Han Sun (4595704)
Shou-Bin Ning (4595707)

August 2018

Figure S1. Flow diagram of patients enrollment. PJS indicates Peutz-Jeghers syndrome. Figue S2. The ...

Additional file 3: of Batten disease: biochemical and molecular characterization revealing novel PPT1 and TPP1 gene mutations in Indian patients

Jayesh Sheth (318977)
Mehul Mistri (318964)
Riddhi Bhavsar (5211767)
Dhairya Pancholi (5211761)
Mahesh Kamate (6080429)
Neerja Gupta (53651)
Madhulika Kabra (53650)
Sanjiv Mehta (6080432)
Sheela Nampoothiri (5229311)
Arpita Thakker (6080435)
Vivek Jain (310927)
Raju Shah (4535845)
Frenny Sheth (318968)

December 2018

ClinVar Accession ID of the novel variants generated in the given study. The variants identified thr...

Additional file 1: of The altered activity of P53 signaling pathway by STK11 gene mutations and its cancer phenotype in Peutz-Jeghers syndrome

Yu-Liang Jiang (4595710)
Zi-Ye Zhao (4595716)
Bai-Rong Li (4595713)
Fu Yang (101882)
Jing Li (10611)
Xiao-Wei Jin (4595701)
Hao Wang (39217)
En-Da Yu (462877)
Shu-Han Sun (4595704)
Shou-Bin Ning (4595707)

August 2018

Table S1. Primers for exon-specific sequencing of STK11 gene. Table S2. Native place of PJS patients...

Additional file 2: of PIK3CA activating mutations are associated with more disseminated disease at presentation and earlier recurrence in glioblastoma

Shota Tanaka (339198)
Tracy Batchelor (6648710)
A. Iafrate (6648713)
Dora Dias-Santagata (128565)
Darrell Borger (192022)
Leif Ellisen (6648716)
Daniel Yang (584075)
David Louis (6648725)
Daniel Cahill (5868119)
Andrew Chi (6648728)

April 2019

Figure S2. Kaplan-Meier curves of OS stratified by PIK3CA mutation. PIK3CA mutant tumors (solid) and...

Angelica Bianco (1461580)
Luigi Bisceglia (13266)
Maria De Caro (5567237)
Valeria Galeandro (5567240)
Patrizia De Bonis (5567243)
Apollonia Tullo (62037)
Stefano Zoccolella (313665)
Silvana Guerriero (5567246)
Vittoria Petruzzella (5567249)

July 2018

Prioritization of mtDNA variants by MToolBox in LHON proband. All potentially deleterious mutations ...

Additional file 2: of Batten disease: biochemical and molecular characterization revealing novel PPT1 and TPP1 gene mutations in Indian patients

Jayesh Sheth (318977)
Mehul Mistri (318964)
Riddhi Bhavsar (5211767)
Dhairya Pancholi (5211761)
Mahesh Kamate (6080429)
Neerja Gupta (53651)
Madhulika Kabra (53650)
Sanjiv Mehta (6080432)
Sheela Nampoothiri (5229311)
Arpita Thakker (6080435)
Vivek Jain (310927)
Raju Shah (4535845)
Frenny Sheth (318968)

December 2018

In silico analysis of the functional effect of the variants identified in the patients with NCL1 and...

Additional file 1: Figure S1. of Novel MASP1 mutations are associated with an expanded phenotype in 3MC1 syndrome

Tahir Atik (824928)
Asuman Koparir (3435422)
Guney Bademci (222766)
Joseph Foster (3435410)
Umut Altunoglu (3435401)
GĂźl Mutlu (3435425)
Sarah Bowdin (524929)
Nursel Elcioglu (214959)
Gulsen Tayfun (3435404)
Sevinc Atik (3435416)
Mustafa Ozen (589386)
Ferda Ozkinay (214965)
Yasemin Alanay (3435407)
Hulya Kayserili (3435413)
Steffen Thiel (12664)
Mustafa Tekin (114701)

September 2015

Pedigrees of the studied families. Figure S2. Electropherograms showing detected pathogenic variants...

Additional file 2: of Identification of mutations in the PI3K-AKT-mTOR signalling pathway in patients with macrocephaly and developmental delay and/or autism

Abstract

Extracted data

Additional file 2: of Identification of mutations in the PI3K-AKT-mTOR signalling pathway in patients with macrocephaly and developmental delay and/or autism

Abstract

Extracted data

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