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Publications

Yingleong Rigel Chan
Publication List

Elaine Lim Publications

Total: 15 results

  • Alzheimer's disease-associated CD83(+) microglia are linked with increased immunoglobulin G4 and human cytomegalovirus in the gut, vagal nerve, and brain

    Thursday, December 19, 2024
    Author(s): Benjamin P Readhead,Diego F Mastroeni,Qi Wang,Maria A Sierra,Camila de Ávila,Tajudeen O Jimoh,Jean-Vianney Haure-Mirande,Kristina E Atanasoff,Jennifer Nolz,Crystal Suazo,Nathaniel J Barton,Adrian R Orszulak,Samantha M Chigas,Khanh Tran,Anne Mirza,Krista Ryon,Jacqueline Proszynski,Deena Najjar,Joel T Dudley,Sean T H Liu,Sam Gandy,Michelle E Ehrlich,Eric Alsop,Jerry Antone,Rebecca Reiman,Cory Funk,Rebecca L Best,Michael Jhatro,Kathy Kamath,John Shon,Timothy F Kowalik,David A Bennett,Winnie S Liang,Geidy E Serrano,Thomas G Beach,Kendall Van Keuren-Jensen,Christopher E Mason,Yingleong Chan,Elaine T Lim,Domenico Tortorella,Eric M Reiman
    Source: Alzheimer's & dementia : the journal of the Alzheimer's Association
    INTRODUCTION: While there may be microbial contributions to Alzheimer's disease (AD), findings have been inconclusive. We recently reported an AD-associated CD83(+) microglia subtype associated with increased immunoglobulin G4 (IgG4) in the transverse colon (TC).

  • Herpes Simplex Virus 1 Infection of Human Brain Organoids and Pancreatic Stem Cell-Islets Drives Organoid-Specific Transcripts Associated with Alzheimer's Disease and Autoimmune Diseases

    Tuesday, December 17, 2024
    Author(s): Jonathan Sundstrom,Emma Vanderleeden,Nathaniel J Barton,Sambra D Redick,Pepper Dawes,Liam F Murray,Meagan N Olson,Khanh Tran,Samantha M Chigas,Adrian R Orszulak,George M Church,Benjamin Readhead,Hyung Suk Oh,David M Harlan,David M Knipe,Jennifer P Wang,Yingleong Chan,Elaine T Lim
    Source: Cells
    Viral infections leading to inflammation have been implicated in several common diseases, such as Alzheimer's disease (AD) and type 1 diabetes (T1D). Of note, herpes simplex virus 1 (HSV-1) has been reported to be associated with AD. We sought to identify the transcriptomic changes due to HSV-1 infection and anti-viral drug (acyclovir, ACV) treatment of HSV-1 infection in dissociated cells from human cerebral organoids (dcOrgs) versus stem cell-derived pancreatic islets (sc-islets) to gain...

  • Reliable multiplex generation of pooled induced pluripotent stem cells

    Tuesday, September 26, 2023
    Author(s): Molly Smullen,Meagan N Olson,Julia M Reichert,Pepper Dawes,Liam F Murray,Christina E Baer,Qi Wang,Benjamin Readhead,George M Church,Elaine T Lim,Yingleong Chan
    Source: Cell reports methods
    Reprogramming somatic cells into pluripotent stem cells (iPSCs) enables the study of systems in vitro. To increase the throughput of reprogramming, we present induction of pluripotency from pooled cells (iPPC)-an efficient, scalable, and reliable reprogramming procedure. Using our deconvolution algorithm that employs pooled sequencing of single-nucleotide polymorphisms (SNPs), we accurately estimated individual donor proportions of the pooled iPSCs. With iPPC, we concurrently reprogrammed over...

  • Editorial for the Neurogenetics and Neurogenomics special issue

    Thursday, July 20, 2023
    Author(s): Elaine T Lim,Yingleong Chan
    Source: Human genetics
    No abstract

  • Modeling of mitochondrial genetic polymorphisms reveals induction of heteroplasmy by pleiotropic disease locus 10398A>G

    Tuesday, June 27, 2023
    Author(s): Molly Smullen,Meagan N Olson,Liam F Murray,Madhusoodhanan Suresh,Guang Yan,Pepper Dawes,Nathaniel J Barton,Jivanna N Mason,Yucheng Zhang,Aria A Fernandez-Fontaine,George M Church,Diego Mastroeni,Qi Wang,Elaine T Lim,Yingleong Chan,Benjamin Readhead
    Source: Scientific reports
    Mitochondrial (MT) dysfunction has been associated with several neurodegenerative diseases including Alzheimer's disease (AD). While MT-copy number differences have been implicated in AD, the effect of MT heteroplasmy on AD has not been well characterized. Here, we analyzed over 1800 whole genome sequencing data from four AD cohorts in seven different tissue types to determine the extent of MT heteroplasmy present. While MT heteroplasmy was present throughout the entire MT genome for blood...

  • FACS-Based Sequencing Approach to Evaluate Cell Type to Genotype Associations Using Cerebral Organoids

    Saturday, June 10, 2023
    Author(s): Liam Murray,Meagan N Olson,Nathaniel Barton,Pepper Dawes,Yingleong Chan,Elaine T Lim
    Source: Methods in molecular biology (Clifton, N.J.)
    Recent technological developments have led to widespread applications of large-scale transcriptomics-based sequencing methods to identify genotype-to-cell type associations. Here we describe a fluorescence-activated cell sorting (FACS)-based sequencing method to utilize CRISPR/Cas9 edited mosaic cerebral organoids to identify or validate genotype-to-cell type associations. Our approach is high-throughput and quantitative and uses internal controls to enable comparisons of the results across...

  • oFlowSeq: a quantitative approach to identify protein coding mutations affecting cell type enrichment using mosaic CRISPR-Cas9 edited cerebral organoids

    Monday, March 06, 2023
    Author(s): Pepper Dawes,Liam F Murray,Meagan N Olson,Nathaniel J Barton,Molly Smullen,Madhusoodhanan Suresh,Guang Yan,Yucheng Zhang,Aria Fernandez-Fontaine,Jay English,Mohammed Uddin,ChangHui Pak,George M Church,Yingleong Chan,Elaine T Lim
    Source: Human genetics
    Cerebral organoids are comprised of diverse cell types found in the developing human brain, and can be leveraged in the identification of critical cell types perturbed by genetic risk variants in common, neuropsychiatric disorders. There is great interest in developing high-throughput technologies to associate genetic variants with cell types. Here, we describe a high-throughput, quantitative approach (oFlowSeq) by utilizing CRISPR-Cas9, FACS sorting, and next-generation sequencing. Using...

  • Orgo-Seq integrates single-cell and bulk transcriptomic data to identify cell type specific-driver genes associated with autism spectrum disorder

    Friday, June 10, 2022
    Author(s): Elaine T Lim,Yingleong Chan,Pepper Dawes,Xiaoge Guo,Serkan Erdin,Derek J C Tai,Songlei Liu,Julia M Reichert,Mannix J Burns,Ying Kai Chan,Jessica J Chiang,Katharina Meyer,Xiaochang Zhang,Christopher A Walsh,Bruce A Yankner,Soumya Raychaudhuri,Joel N Hirschhorn,James F Gusella,Michael E Talkowski,George M Church
    Source: Nature communications
    Cerebral organoids can be used to gain insights into cell type specific processes perturbed by genetic variants associated with neuropsychiatric disorders. However, robust and scalable phenotyping of organoids remains challenging. Here, we perform RNA sequencing on 71 samples comprising 1,420 cerebral organoids from 25 donors, and describe a framework (Orgo-Seq) to integrate bulk RNA and single-cell RNA sequence data. We apply Orgo-Seq to 16p11.2 deletions and 15q11-13 duplications, two loci...

  • Engineering adeno-associated viral vectors to evade innate immune and inflammatory responses

    Thursday, February 11, 2021
    Author(s): Ying Kai Chan,Sean K Wang,Colin J Chu,David A Copland,Alexander J Letizia,Helena Costa Verdera,Jessica J Chiang,Meher Sethi,May K Wang,William J Neidermyer,Yingleong Chan,Elaine T Lim,Amanda R Graveline,Melinda Sanchez,Ryan F Boyd,Thomas S Vihtelic,Rolando Gian Carlo O Inciong,Jared M Slain,Priscilla J Alphonse,Yunlu Xue,Lindsey R Robinson-McCarthy,Jenny M Tam,Maha H Jabbar,Bhubanananda Sahu,Janelle F Adeniran,Manish Muhuri,Phillip W L Tai,Jun Xie,Tyler B Krause,Andyna Vernet,Matthew Pezone,Ru Xiao,Tina Liu,Wei Wang,Henry J Kaplan,Guangping Gao,Andrew D Dick,Federico Mingozzi,Maureen A McCall,Constance L Cepko,George M Church
    Source: Science translational medicine
    Nucleic acids are used in many therapeutic modalities, including gene therapy, but their ability to trigger host immune responses in vivo can lead to decreased safety and efficacy. In the case of adeno-associated viral (AAV) vectors, studies have shown that the genome of the vector activates Toll-like receptor 9 (TLR9), a pattern recognition receptor that senses foreign DNA. Here, we engineered AAV vectors to be intrinsically less immunogenic by incorporating short DNA oligonucleotides that...

  • Publisher Correction: Rates, distribution and implications of postzygotic mosaic mutations in autism spectrum disorder

    Thursday, July 16, 2020
    Author(s): Elaine T Lim,Mohammed Uddin,Silvia De Rubeis,Yingleong Chan,Anne S Kamumbu,Xiaochang Zhang,Alissa M D'Gama,Sonia N Kim,Robert Sean Hill,Arthur P Goldberg,Christopher Poultney,Nancy J Minshew,Itaru Kushima,Branko Aleksic,Norio Ozaki,Mara Parellada,Celso Arango,Maria J Penzol,Angel Carracedo,Alexander Kolevzon,Christina M Hultman,Lauren A Weiss,Menachem Fromer,Andreas G Chiocchetti,Christine M Freitag,Autism Sequencing Consortium,George M Church,Stephen W Scherer,Joseph D Buxbaum,Christopher A Walsh
    Source: Nature neuroscience
    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

  • An enhanced CRISPR repressor for targeted mammalian gene regulation

    Wednesday, July 18, 2018
    Author(s): Nan Cher Yeo,Alejandro Chavez,Alissa Lance-Byrne,Yingleong Chan,David Menn,Denitsa Milanova,Chih-Chung Kuo,Xiaoge Guo,Sumana Sharma,Angela Tung,Ryan J Cecchi,Marcelle Tuttle,Swechchha Pradhan,Elaine T Lim,Noah Davidsohn,Mo R Ebrahimkhani,James J Collins,Nathan E Lewis,Samira Kiani,George M Church
    Source: Nature methods
    The RNA-guided endonuclease Cas9 can be converted into a programmable transcriptional repressor, but inefficiencies in target-gene silencing have limited its utility. Here we describe an improved Cas9 repressor based on the C-terminal fusion of a rationally designed bipartite repressor domain, KRAB-MeCP2, to nuclease-dead Cas9. We demonstrate the system's superiority in silencing coding and noncoding genes, simultaneously repressing a series of target genes, improving the results of single and...

  • High-throughput creation and functional profiling of DNA sequence variant libraries using CRISPR-Cas9 in yeast

    Wednesday, May 23, 2018
    Author(s): Xiaoge Guo,Alejandro Chavez,Angela Tung,Yingleong Chan,Christian Kaas,Yi Yin,Ryan Cecchi,Santiago Lopez Garnier,Eric D Kelsic,Max Schubert,James E DiCarlo,James J Collins,George M Church
    Source: Nature biotechnology
    Construction and characterization of large genetic variant libraries is essential for understanding genome function, but remains challenging. Here, we introduce a Cas9-based approach for generating pools of mutants with defined genetic alterations (deletions, substitutions, and insertions) with an efficiency of 80-100% in yeast, along with methods for tracking their fitness en masse. We demonstrate the utility of our approach by characterizing the DNA helicase SGS1 with small tiling deletion...

  • Enabling multiplexed testing of pooled donor cells through whole-genome sequencing

    Saturday, April 21, 2018
    Author(s): Yingleong Chan,Ying Kai Chan,Daniel B Goodman,Xiaoge Guo,Alejandro Chavez,Elaine T Lim,George M Church
    Source: Genome medicine
    We describe a method that enables the multiplex screening of a pool of many different donor cell lines. Our method accurately predicts each donor proportion from the pool without requiring the use of unique DNA barcodes as markers of donor identity. Instead, we take advantage of common single nucleotide polymorphisms, whole-genome sequencing, and an algorithm to calculate the proportions from the sequencing data. By testing using simulated and real data, we showed that our method robustly...

  • Rates, distribution and implications of postzygotic mosaic mutations in autism spectrum disorder

    Tuesday, July 18, 2017
    Author(s): Elaine T Lim,Mohammed Uddin,Silvia De Rubeis,Yingleong Chan,Anne S Kamumbu,Xiaochang Zhang,Alissa M D'Gama,Sonia N Kim,Robert Sean Hill,Arthur P Goldberg,Christopher Poultney,Nancy J Minshew,Itaru Kushima,Branko Aleksic,Norio Ozaki,Mara Parellada,Celso Arango,Maria J Penzol,Angel Carracedo,Alexander Kolevzon,Christina M Hultman,Lauren A Weiss,Menachem Fromer,Andreas G Chiocchetti,Christine M Freitag,Autism Sequencing Consortium,George M Church,Stephen W Scherer,Joseph D Buxbaum,Christopher A Walsh
    Source: Nature neuroscience
    We systematically analyzed postzygotic mutations (PZMs) in whole-exome sequences from the largest collection of trios (5,947) with autism spectrum disorder (ASD) available, including 282 unpublished trios, and performed resequencing using multiple independent technologies. We identified 7.5% of de novo mutations as PZMs, 83.3% of which were not described in previous studies. Damaging, nonsynonymous PZMs within critical exons of prenatally expressed genes were more common in ASD probands than...

  • An unbiased index to quantify participant's phenotypic contribution to an open-access cohort

    Saturday, April 08, 2017
    Author(s): Yingleong Chan,Michael Tung,Alexander S Garruss,Sarah W Zaranek,Ying Kai Chan,Jeantine E Lunshof,Alexander W Zaranek,Madeleine P Ball,Michael F Chou,Elaine T Lim,George M Church
    Source: Scientific reports
    The Personal Genome Project (PGP) is an effort to enroll many participants to create an open-access repository of genome, health and trait data for research. However, PGP participants are not enrolled for studying any specific traits and participants choose the phenotypes to disclose. To measure the extent and willingness and to encourage and guide participants to contribute phenotypes, we developed an algorithm to score and rank the phenotypes and participants of the PGP. The scoring algorithm...
Total: 15 results

  • Alzheimer's disease-associated CD83(+) microglia are linked with increased immunoglobulin G4 and human cytomegalovirus in the gut, vagal nerve, and brain

    Thursday, December 19, 2024
    Author(s): Benjamin P Readhead,Diego F Mastroeni,Qi Wang,Maria A Sierra,Camila de Ávila,Tajudeen O Jimoh,Jean-Vianney Haure-Mirande,Kristina E Atanasoff,Jennifer Nolz,Crystal Suazo,Nathaniel J Barton,Adrian R Orszulak,Samantha M Chigas,Khanh Tran,Anne Mirza,Krista Ryon,Jacqueline Proszynski,Deena Najjar,Joel T Dudley,Sean T H Liu,Sam Gandy,Michelle E Ehrlich,Eric Alsop,Jerry Antone,Rebecca Reiman,Cory Funk,Rebecca L Best,Michael Jhatro,Kathy Kamath,John Shon,Timothy F Kowalik,David A Bennett,Winnie S Liang,Geidy E Serrano,Thomas G Beach,Kendall Van Keuren-Jensen,Christopher E Mason,Yingleong Chan,Elaine T Lim,Domenico Tortorella,Eric M Reiman
    Source: Alzheimer's & dementia : the journal of the Alzheimer's Association
    INTRODUCTION: While there may be microbial contributions to Alzheimer's disease (AD), findings have been inconclusive. We recently reported an AD-associated CD83(+) microglia subtype associated with increased immunoglobulin G4 (IgG4) in the transverse colon (TC).

  • Herpes Simplex Virus 1 Infection of Human Brain Organoids and Pancreatic Stem Cell-Islets Drives Organoid-Specific Transcripts Associated with Alzheimer's Disease and Autoimmune Diseases

    Tuesday, December 17, 2024
    Author(s): Jonathan Sundstrom,Emma Vanderleeden,Nathaniel J Barton,Sambra D Redick,Pepper Dawes,Liam F Murray,Meagan N Olson,Khanh Tran,Samantha M Chigas,Adrian R Orszulak,George M Church,Benjamin Readhead,Hyung Suk Oh,David M Harlan,David M Knipe,Jennifer P Wang,Yingleong Chan,Elaine T Lim
    Source: Cells
    Viral infections leading to inflammation have been implicated in several common diseases, such as Alzheimer's disease (AD) and type 1 diabetes (T1D). Of note, herpes simplex virus 1 (HSV-1) has been reported to be associated with AD. We sought to identify the transcriptomic changes due to HSV-1 infection and anti-viral drug (acyclovir, ACV) treatment of HSV-1 infection in dissociated cells from human cerebral organoids (dcOrgs) versus stem cell-derived pancreatic islets (sc-islets) to gain...

  • LONG TERM OUTCOMES OF GANGLIONATED-PLEXUS ABLATION AS SOLE THERAPY FOR PAROXYSMAL ATRIAL FIBRILLATION

    Sunday, December 15, 2024
    Author(s): Jamie Kay,Min-Young Kim,Clare Coyle,David R Tomlinson,Louisa Malcolme-Lawes,Elaine Lim,Michael Fudge,Ian J Wright,Michael Koa-Wing,Fu Siong Ng,Norman A Qureshi,Zachary I Whinnett,Nicholas S Peters,Gurpreet Dhillon,Ross J Hunter,Phang Boon Lim,Nicholas W F Linton,Prapa Kanagaratnam
    Source: Heart rhythm
    No abstract

  • Cost-minimization analysis comparing subcutaneous trastuzumab at home with intravenous trastuzumab for HER2-positive breast cancer in Singapore

    Tuesday, November 12, 2024
    Author(s): Yanting Ouyang,Han Yi Lee,Fun Loon Leong,Han Jieh Tey,Vivianne Shih,Elaine Hsuen Lim,Nicholas Graves
    Source: Therapeutic advances in medical oncology
    CONCLUSION: Treatment of breast cancer with Homecare SC Herceptin is a cost-saving option compared to IV Herceptin.

  • Efficacy and safety of sacituzumab govitecan Trop-2-targeted antibody-drug conjugate in solid tumors and UGT1A1*28 polymorphism: a systematic review and meta-analysis

    Monday, November 11, 2024
    Author(s): Rehena Sultana,Sylvia Chen,Elaine Hsuen Lim,Rebecca Dent,Balram Chowbay
    Source: BJC reports
    CONCLUSION: Our systematic review and meta-analysis confirmed that SG confers good clinical activity in certain solid tumor types and was tolerable with minimal adverse events. The potential utility of UGT1A1*28 genotyping in predicting clinical response and outcomes could not be determined due to the limited number of studies with available UGT1A1 genotype data.

  • Deciphering tumour microenvironment and elucidating the origin of cancer cells in ovarian clear cell carcinoma

    Friday, August 16, 2024
    Author(s): Uma S Kamaraj,Pradeep Gautam,Terence Cheng,Tham Su Chin,Sun Kuie Tay,Tew Hong Ho,Ravichandran Nadarajah,Ronald Chin Hong Goh,Shing Lih Wong,Sangeeta Mantoo,Inny Busmanis,Hu Li,Minh Tn Le,Qi-Jing Li,Elaine Hsuen Lim,Yuin-Han Loh
    Source: bioRxiv : the preprint server for biology
    Ovarian clear cell carcinoma (CCC) has an East Asian preponderance. It is associated with endometriosis, a benign condition where endometrial (inner lining of the uterus) tissue is found outside the uterus and on the peritoneal surface, in the abdominal or pelvic space. CCC is relatively more resistant to conventional chemotherapy compared to other ovarian cancer subtypes and is associated with a poorer prognosis. In this study, we recruited and obtained tumour tissues from seven patients across...

  • Mapping recurrent mosaic copy number variation in human neurons

    Friday, May 17, 2024
    Author(s): Chen Sun,Kunal Kathuria,Sarah B Emery,ByungJun Kim,Ian E Burbulis,Joo Heon Shin,Brain Somatic Mosaicism Network,Daniel R Weinberger,John V Moran,Jeffrey M Kidd,Ryan E Mills,Michael J McConnell
    Source: Nature communications
    When somatic cells acquire complex karyotypes, they often are removed by the immune system. Mutant somatic cells that evade immune surveillance can lead to cancer. Neurons with complex karyotypes arise during neurotypical brain development, but neurons are almost never the origin of brain cancers. Instead, somatic mutations in neurons can bring about neurodevelopmental disorders, and contribute to the polygenic landscape of neuropsychiatric and neurodegenerative disease. A subset of human...

  • Combined aerobic and strength exercise training on biological ageing in Singaporean breast cancer patients: protocol for the Breast Cancer Exercise Intervention (BREXINT) Pilot Study

    Thursday, March 28, 2024
    Author(s): Patrick Henry Sebastian Sitjar,Si Ying Tan,Mabel Wong,Jingmei Li,Rufaihah Binte Abdul Jalil,Huizhen Aw,Elaine Hsuen Lim,Jorming Goh
    Source: GeroScience
    Breast cancer (BC) is the most prominent cancer amongst women, but fortunately, early diagnosis and advances in multimodality treatments have improved patient survivability. Cancer survivors, however, experience increased biological ageing which may accelerate other co-morbidities. Exercise intervention is a promising clinical adjuvant approach to improve BC patients' physiological function, recovery from treatment, and quality of life. However, the effects of combined aerobic and strength...

  • Expression of ALS-PFN1 impairs vesicular degradation in iPSC-derived microglia

    Thursday, March 21, 2024
    Author(s): Salome Funes,Jonathan Jung,Del Hayden Gadd,Michelle Mosqueda,Jianjun Zhong,None Shankaracharya,Matthew Unger,Karly Stallworth,Debra Cameron,Melissa S Rotunno,Pepper Dawes,Megan Fowler-Magaw,Pamela J Keagle,Justin A McDonough,Sivakumar Boopathy,Miguel Sena-Esteves,Jeffrey A Nickerson,Cathleen Lutz,William C Skarnes,Elaine T Lim,Dorothy P Schafer,Francesca Massi,John E Landers,Daryl A Bosco
    Source: Nature communications
    Microglia play a pivotal role in neurodegenerative disease pathogenesis, but the mechanisms underlying microglia dysfunction and toxicity remain to be elucidated. To investigate the effect of neurodegenerative disease-linked genes on the intrinsic properties of microglia, we studied microglia-like cells derived from human induced pluripotent stem cells (iPSCs), termed iMGs, harboring mutations in profilin-1 (PFN1) that are causative for amyotrophic lateral sclerosis (ALS). ALS-PFN1 iMGs...

  • Cost-effectiveness analysis of add-on pertuzumab to trastuzumab biosimilar and chemotherapy as neoadjuvant treatment for human epidermal growth receptor 2-positive early breast cancer patients in Singapore

    Tuesday, January 30, 2024
    Author(s): Elaine Hsuen Lim,Andrew Lim,Jasmeet Singh Khara,John Cheong,Jek Fong,Sivabalan Sivanesan,Matt Griffiths,Emma New,Soo Chin Lee
    Source: Expert review of pharmacoeconomics & outcomes research
    CONCLUSIONS: This model demonstrated that the long-term clinical impact of early pertuzumab use, particularly the avoidance of metastatic disease and thus avoidance of higher costs and mortality rates, make neoadjuvant pertuzumab a cost-effective option in the management of patients with HER2+ breast cancer in Singapore.

  • Mutational spectrum and phenotypic variability of Duchenne muscular dystrophy and related disorders in a Bangladeshi population

    Wednesday, December 06, 2023
    Author(s): Shaoli Sarker,Tamannyat Binte Eshaque,Anjana Soorajkumar,Nasna Nassir,Binte Zehra,Shayla Imam Kanta,Md Atikur Rahaman,Amirul Islam,Shimu Akter,Mohammad Kawsar Ali,Rabeya Akter Mim,K M Furkan Uddin,Mohammod Shah Jahan Chowdhury,Nusrat Shams,Md Abdul Baqui,Elaine T Lim,Hosneara Akter,Marc Woodbury-Smith,Mohammed Uddin
    Source: Scientific reports
    Duchenne muscular dystrophy (DMD) is a severe rare neuromuscular disorder caused by mutations in the X-linked dystrophin gene. Several mutations have been identified, yet the full mutational spectrum, and their phenotypic consequences, will require genotyping across different populations. To this end, we undertook the first detailed genotype and phenotype characterization of DMD in the Bangladeshi population. We investigated the rare mutational and phenotypic spectrum of the DMD gene in 36...

  • Alterations to DNA methylation patterns induced by chemotherapy treatment are associated with negative impacts on the olfactory pathway

    Tuesday, November 07, 2023
    Author(s): Peh Joo Ho,Alexis Jiaying Khng,Benita Kiat-Tee Tan,Geok Hoon Lim,Su-Ming Tan,Veronique Kiak Mien Tan,Ryan Shea Ying Cong Tan,Elaine Hsuen Lim,Philip Tsau-Choong Iau,Ying Jia Chew,Yi Ying Lim,Mikael Hartman,Ern Yu Tan,Jingmei Li
    Source: Breast cancer research : BCR
    CONCLUSION: The enrichment of imprinted genes within biological processes and pathways suggests a biological mechanism by which chemotherapy could affect the perception of smell.

  • Reliable multiplex generation of pooled induced pluripotent stem cells

    Tuesday, September 26, 2023
    Author(s): Molly Smullen,Meagan N Olson,Julia M Reichert,Pepper Dawes,Liam F Murray,Christina E Baer,Qi Wang,Benjamin Readhead,George M Church,Elaine T Lim,Yingleong Chan
    Source: Cell reports methods
    Reprogramming somatic cells into pluripotent stem cells (iPSCs) enables the study of systems in vitro. To increase the throughput of reprogramming, we present induction of pluripotency from pooled cells (iPPC)-an efficient, scalable, and reliable reprogramming procedure. Using our deconvolution algorithm that employs pooled sequencing of single-nucleotide polymorphisms (SNPs), we accurately estimated individual donor proportions of the pooled iPSCs. With iPPC, we concurrently reprogrammed over...

  • Author Correction: Machine learning reveals bilateral distribution of somatic L1 insertions in human neurons and glia

    Wednesday, August 30, 2023
    Author(s): Xiaowei Zhu,Bo Zhou,Reenal Pattni,Kelly Gleason,Chunfeng Tan,Agnieszka Kalinowski,Steven Sloan,Anna-Sophie Fiston-Lavier,Jessica Mariani,Dmitri Petrov,Ben A Barres,Laramie Duncan,Alexej Abyzov,Hannes Vogel,Brain Somatic Mosaicism Network,John V Moran,Flora M Vaccarino,Carol A Tamminga,Douglas F Levinson,Alexander E Urban
    Source: Nature neuroscience
    No abstract

  • Author Correction: The landscape of somatic mutation in cerebral cortex of autistic and neurotypical individuals revealed by ultra-deep whole-genome sequencing

    Tuesday, August 29, 2023
    Author(s): Rachel E Rodin,Yanmei Dou,Minseok Kwon,Maxwell A Sherman,Alissa M D'Gama,Ryan N Doan,Lariza M Rento,Kelly M Girskis,Craig L Bohrson,Sonia N Kim,Ajay Nadig,Lovelace J Luquette,Doga C Gulhan,Brain Somatic Mosaicism Network,Peter J Park,Christopher A Walsh
    Source: Nature neuroscience
    No abstract