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Papers by Enrique Alvirez

Research paper thumbnail of Additional file 1: of Low-cost HPV testing and the prevalence of cervical infection in asymptomatic populations in Guatemala

Figure S1. Amplification of HPV positive and negative cell line genomic DNA by Touchdown PCR usin... more Figure S1. Amplification of HPV positive and negative cell line genomic DNA by Touchdown PCR using BS GP5+/6+ primers. A dilution series of an HPV positive cell line (HeLa), HPV negative (HEK293) and HPV-status unknown cell lines were amplified by touchdown PCR with both HPV primer sets and a globin primer pair, and run on 1.5% agarose gels. Figure S2. Touchdown PCR from swab cell lysate, (A): Lane 1.- Lane 4 HPV positive control with input DNA 1 ng, 0.1 ng, 0.01 ng and 0.001 ng; Lane 5. HPV negative control (cell line); Lane 6. no template control. Lane 7 to Lane 16 indicate unknown swab samples. M indicate the DNA ladder marker. Touchdown PCR from HPV positive swabs by Hybribio Assay (B): Lane 1. – Lane 18 are swab cell lysate; Lane 19. HPV positive control (cell line); Lane 20. HPV negative control (cell line); Lane 21. no template control. The samples were amplified with the BSGP5+/6+ primers. (DOCX 2548 kb)

Research paper thumbnail of Extrachromosomal Amplification of Human Papillomavirus Episomes as a Mechanism of Cervical Carcinogenesis

SummaryIntegration of Human Papillomaviruses (HPV) is an important mechanism of carcinogenesis bu... more SummaryIntegration of Human Papillomaviruses (HPV) is an important mechanism of carcinogenesis but is absent in a significant fraction of HPV16+ tumors. We applied long-read whole-genome sequencing (WGS) to cervical cancer cell lines and tumors. In two HPV16+ cell lines, we identified large tandem arrays of full-length and truncated viral genomes integrated into multiple locations indicating formation as extrachromosomal DNA (HPV superspreading). An HPV16+ cell line with episomal DNA has tandem arrays of full-length, truncated, and rearranged HPV16 genomes (multimer episomes). WGS of HPV16+ cervical tumors revealed that 11/20 with only episomal HPV (EP) have intact monomer episomes. The remaining nine EP tumors have multimer and rearranged HPV genomes. Most HPV rearrangements disrupt the E1 and E2 genes, and EP tumors overexpress the E6 and E7 viral oncogenes. Tumors with both episomal and integrated HPV16 display multimer episomes and concatemers of human and viral sequences. One t...

Research paper thumbnail of The D2 and D3 Sublineages of Human Papilloma Virus 16–Positive Cervical Cancer in Guatemala Differ in Integration Rate and Age of Diagnosis

Cancer Research, 2020

Human papillomavirus (HPV) 16 displays substantial sequence variation; four HPV16 lineages (A, B,... more Human papillomavirus (HPV) 16 displays substantial sequence variation; four HPV16 lineages (A, B, C, and D) have been described as well as multiple sublineages. To identify molecular events associated with HPV16 carcinogenesis, we evaluated viral variation, the integration of HPV16, and somatic mutation in 96 cervical cancer samples from Guatemala. A total of 65% (62/96) of the samples had integrated HPV16 sequences and integration was associated with an earlier age of diagnosis and premenopausal disease. HPV16 integration sites were broadly distributed in the genome, but in one tumor, HPV16 integrated into the promoter of the IFN regulatory factor 4 (IRF4) gene, which plays an important role in the regulation of the IFN response to viral infection. The HPV16 D2 and D3 sublineages were found in 23% and 30% of the tumors, respectively, and were significantly associated with adenocarcinoma. D2-positive tumors had a higher rate of integration, earlier age of diagnosis, and a lower rate...

Research paper thumbnail of Correction to: Low-cost HPV testing and the prevalence of cervical infection in asymptomatic populations in Guatemala

BMC Cancer, 2020

Following publication of the original article [1], an error was reported in the tagging of Joël F... more Following publication of the original article [1], an error was reported in the tagging of Joël Fokom Domgue in the author group. The tagging in this correction article has been fixed.

Research paper thumbnail of Human papillomavirus 16 positive cervical cancer in Guatemala: The D2 and D3 sublineages differ in integration rate and age of diagnosis

Human papillomavirus (HPV) 16 displays substantial sequence variation; four HPV16 lineages (A, B,... more Human papillomavirus (HPV) 16 displays substantial sequence variation; four HPV16 lineages (A, B, C, D) have been described, as well as multiple sub-lineages. To identify molecular events associated with HPV16 carcinogenesis we evaluated viral variation, the integration of HPV16, and somatic mutation in 96 cervical cancer samples from Guatemala. A total of 64% (60/94) of the samples had integrated HPV16 sequences, and integration was associated with an earlier age of diagnosis (P=0.0007) and pre-menopausal disease. HPV16 integration sites were broadly distributed in the genome but in one tumor, HPV16 integrated into the promoter of the interferon regulatory factor 4 (IRF4) gene, which plays an important role in the regulation of the interferon response to viral infection. The HPV16 D2 and D3 sub-lineages were found in 23% and 30% of the tumors, respectively and were significantly associated with adenocarcinoma. D2-positive tumors had a higher rate of integration (P=0.011), earlier a...

Research paper thumbnail of Low-cost HPV testing and the prevalence of cervical infection in asymptomatic populations in Guatemala

ABSTRACTBackgroundA low cost and accurate method for detecting high-risk (HR) HPV is important to... more ABSTRACTBackgroundA low cost and accurate method for detecting high-risk (HR) HPV is important to permit HPV testing for cervical cancer prevention. We validated a low-cost commercially available HPV method (H13, Hybribio, Hong Kong) and determined the distribution of HPV infections in over 1717 cancer-free women in Guatemala.MethodsH13 results were compared with two more established HPV tests: (Xpert™ (Cepheid) and SPF10-LIPA25™ (DDL)) in 40 mainly known positive specimens. HR-HPV was detected in cervical samples from 1717 cancer-free women receiving Pap smears using the Hybribio™ realtime PCR assay of 13 HR types. Selected HPV positive samples were sequenced to determine viral type.ResultsThe Hybribio H13 Assay showed 93% identical results with Xpert, and 89% with SPF10-LIPA25. A total of 13% (226/1717) of women tested HPV+. The highest prevalence was found in younger women (<30 years, 22 %) and older ones (≥60 years, 15%). The six most common HR-HPV types among the 148 HPV+ ty...

Research paper thumbnail of Genome Analysis of Latin American Cervical Cancer: Frequent Activation of the PIK3CA Pathway

Clinical cancer research : an official journal of the American Association for Cancer Research, Jan 16, 2015

Cervical cancer is one of the most common causes of cancer mortality for women living in poverty,... more Cervical cancer is one of the most common causes of cancer mortality for women living in poverty, causing over 28,000 deaths annually in Latin America and 266,000 worldwide. To better understand the molecular basis of the disease we ascertained blood and tumor samples from Guatemala and Venezuela and performed genomic characterization. We performed HPV typing and identified somatically mutated genes using exome and ultra-deep targeted sequencing with confirmation in samples from Mexico. Copy number changes were also assessed in the exome sequence. Cervical cancer cases in Guatemala and Venezuela have an average age-of-diagnosis of 50 years, and 5.6 children. Analysis of 675 tumors revealed activation of PIK3CA and other phosphatidyl inositol (PI3K)/AKT pathway genes in 31% of squamous carcinomas and 24% of adeno- and adenosquamous tumors, predominantly at two sites (E542K, E545K) in the helical domain of the PIK3CA gene. This distribution of PIK3CA mutations is distinct from most ot...

Research paper thumbnail of Abstract C121: Genomic characterization of invasive cervical cancer in Guatemala and Venezuela: Common activation of the PIK3CA pathway

Molecular Cancer Therapeutics

Research paper thumbnail of Genome Analysis of Latin American Cervical Cancer: Frequent Activation of the PIK3CA Pathway

Clinical cancer research : an official journal of the American Association for Cancer Research, Jan 16, 2015

Cervical cancer is one of the most common causes of cancer mortality for women living in poverty,... more Cervical cancer is one of the most common causes of cancer mortality for women living in poverty, causing over 28,000 deaths annually in Latin America and 266,000 worldwide. To better understand the molecular basis of the disease we ascertained blood and tumor samples from Guatemala and Venezuela and performed genomic characterization. We performed HPV typing and identified somatically mutated genes using exome and ultra-deep targeted sequencing with confirmation in samples from Mexico. Copy number changes were also assessed in the exome sequence. Cervical cancer cases in Guatemala and Venezuela have an average age-of-diagnosis of 50 years, and 5.6 children. Analysis of 675 tumors revealed activation of PIK3CA and other phosphatidyl inositol (PI3K)/AKT pathway genes in 31% of squamous carcinomas and 24% of adeno- and adenosquamous tumors, predominantly at two sites (E542K, E545K) in the helical domain of the PIK3CA gene. This distribution of PIK3CA mutations is distinct from most ot...

Research paper thumbnail of Additional file 1: of Low-cost HPV testing and the prevalence of cervical infection in asymptomatic populations in Guatemala

Figure S1. Amplification of HPV positive and negative cell line genomic DNA by Touchdown PCR usin... more Figure S1. Amplification of HPV positive and negative cell line genomic DNA by Touchdown PCR using BS GP5+/6+ primers. A dilution series of an HPV positive cell line (HeLa), HPV negative (HEK293) and HPV-status unknown cell lines were amplified by touchdown PCR with both HPV primer sets and a globin primer pair, and run on 1.5% agarose gels. Figure S2. Touchdown PCR from swab cell lysate, (A): Lane 1.- Lane 4 HPV positive control with input DNA 1 ng, 0.1 ng, 0.01 ng and 0.001 ng; Lane 5. HPV negative control (cell line); Lane 6. no template control. Lane 7 to Lane 16 indicate unknown swab samples. M indicate the DNA ladder marker. Touchdown PCR from HPV positive swabs by Hybribio Assay (B): Lane 1. – Lane 18 are swab cell lysate; Lane 19. HPV positive control (cell line); Lane 20. HPV negative control (cell line); Lane 21. no template control. The samples were amplified with the BSGP5+/6+ primers. (DOCX 2548 kb)

Research paper thumbnail of Extrachromosomal Amplification of Human Papillomavirus Episomes as a Mechanism of Cervical Carcinogenesis

SummaryIntegration of Human Papillomaviruses (HPV) is an important mechanism of carcinogenesis bu... more SummaryIntegration of Human Papillomaviruses (HPV) is an important mechanism of carcinogenesis but is absent in a significant fraction of HPV16+ tumors. We applied long-read whole-genome sequencing (WGS) to cervical cancer cell lines and tumors. In two HPV16+ cell lines, we identified large tandem arrays of full-length and truncated viral genomes integrated into multiple locations indicating formation as extrachromosomal DNA (HPV superspreading). An HPV16+ cell line with episomal DNA has tandem arrays of full-length, truncated, and rearranged HPV16 genomes (multimer episomes). WGS of HPV16+ cervical tumors revealed that 11/20 with only episomal HPV (EP) have intact monomer episomes. The remaining nine EP tumors have multimer and rearranged HPV genomes. Most HPV rearrangements disrupt the E1 and E2 genes, and EP tumors overexpress the E6 and E7 viral oncogenes. Tumors with both episomal and integrated HPV16 display multimer episomes and concatemers of human and viral sequences. One t...

Research paper thumbnail of The D2 and D3 Sublineages of Human Papilloma Virus 16–Positive Cervical Cancer in Guatemala Differ in Integration Rate and Age of Diagnosis

Cancer Research, 2020

Human papillomavirus (HPV) 16 displays substantial sequence variation; four HPV16 lineages (A, B,... more Human papillomavirus (HPV) 16 displays substantial sequence variation; four HPV16 lineages (A, B, C, and D) have been described as well as multiple sublineages. To identify molecular events associated with HPV16 carcinogenesis, we evaluated viral variation, the integration of HPV16, and somatic mutation in 96 cervical cancer samples from Guatemala. A total of 65% (62/96) of the samples had integrated HPV16 sequences and integration was associated with an earlier age of diagnosis and premenopausal disease. HPV16 integration sites were broadly distributed in the genome, but in one tumor, HPV16 integrated into the promoter of the IFN regulatory factor 4 (IRF4) gene, which plays an important role in the regulation of the IFN response to viral infection. The HPV16 D2 and D3 sublineages were found in 23% and 30% of the tumors, respectively, and were significantly associated with adenocarcinoma. D2-positive tumors had a higher rate of integration, earlier age of diagnosis, and a lower rate...

Research paper thumbnail of Correction to: Low-cost HPV testing and the prevalence of cervical infection in asymptomatic populations in Guatemala

BMC Cancer, 2020

Following publication of the original article [1], an error was reported in the tagging of Joël F... more Following publication of the original article [1], an error was reported in the tagging of Joël Fokom Domgue in the author group. The tagging in this correction article has been fixed.

Research paper thumbnail of Human papillomavirus 16 positive cervical cancer in Guatemala: The D2 and D3 sublineages differ in integration rate and age of diagnosis

Human papillomavirus (HPV) 16 displays substantial sequence variation; four HPV16 lineages (A, B,... more Human papillomavirus (HPV) 16 displays substantial sequence variation; four HPV16 lineages (A, B, C, D) have been described, as well as multiple sub-lineages. To identify molecular events associated with HPV16 carcinogenesis we evaluated viral variation, the integration of HPV16, and somatic mutation in 96 cervical cancer samples from Guatemala. A total of 64% (60/94) of the samples had integrated HPV16 sequences, and integration was associated with an earlier age of diagnosis (P=0.0007) and pre-menopausal disease. HPV16 integration sites were broadly distributed in the genome but in one tumor, HPV16 integrated into the promoter of the interferon regulatory factor 4 (IRF4) gene, which plays an important role in the regulation of the interferon response to viral infection. The HPV16 D2 and D3 sub-lineages were found in 23% and 30% of the tumors, respectively and were significantly associated with adenocarcinoma. D2-positive tumors had a higher rate of integration (P=0.011), earlier a...

Research paper thumbnail of Low-cost HPV testing and the prevalence of cervical infection in asymptomatic populations in Guatemala

ABSTRACTBackgroundA low cost and accurate method for detecting high-risk (HR) HPV is important to... more ABSTRACTBackgroundA low cost and accurate method for detecting high-risk (HR) HPV is important to permit HPV testing for cervical cancer prevention. We validated a low-cost commercially available HPV method (H13, Hybribio, Hong Kong) and determined the distribution of HPV infections in over 1717 cancer-free women in Guatemala.MethodsH13 results were compared with two more established HPV tests: (Xpert™ (Cepheid) and SPF10-LIPA25™ (DDL)) in 40 mainly known positive specimens. HR-HPV was detected in cervical samples from 1717 cancer-free women receiving Pap smears using the Hybribio™ realtime PCR assay of 13 HR types. Selected HPV positive samples were sequenced to determine viral type.ResultsThe Hybribio H13 Assay showed 93% identical results with Xpert, and 89% with SPF10-LIPA25. A total of 13% (226/1717) of women tested HPV+. The highest prevalence was found in younger women (<30 years, 22 %) and older ones (≥60 years, 15%). The six most common HR-HPV types among the 148 HPV+ ty...

Research paper thumbnail of Genome Analysis of Latin American Cervical Cancer: Frequent Activation of the PIK3CA Pathway

Clinical cancer research : an official journal of the American Association for Cancer Research, Jan 16, 2015

Cervical cancer is one of the most common causes of cancer mortality for women living in poverty,... more Cervical cancer is one of the most common causes of cancer mortality for women living in poverty, causing over 28,000 deaths annually in Latin America and 266,000 worldwide. To better understand the molecular basis of the disease we ascertained blood and tumor samples from Guatemala and Venezuela and performed genomic characterization. We performed HPV typing and identified somatically mutated genes using exome and ultra-deep targeted sequencing with confirmation in samples from Mexico. Copy number changes were also assessed in the exome sequence. Cervical cancer cases in Guatemala and Venezuela have an average age-of-diagnosis of 50 years, and 5.6 children. Analysis of 675 tumors revealed activation of PIK3CA and other phosphatidyl inositol (PI3K)/AKT pathway genes in 31% of squamous carcinomas and 24% of adeno- and adenosquamous tumors, predominantly at two sites (E542K, E545K) in the helical domain of the PIK3CA gene. This distribution of PIK3CA mutations is distinct from most ot...

Research paper thumbnail of Abstract C121: Genomic characterization of invasive cervical cancer in Guatemala and Venezuela: Common activation of the PIK3CA pathway

Molecular Cancer Therapeutics

Research paper thumbnail of Genome Analysis of Latin American Cervical Cancer: Frequent Activation of the PIK3CA Pathway

Clinical cancer research : an official journal of the American Association for Cancer Research, Jan 16, 2015

Cervical cancer is one of the most common causes of cancer mortality for women living in poverty,... more Cervical cancer is one of the most common causes of cancer mortality for women living in poverty, causing over 28,000 deaths annually in Latin America and 266,000 worldwide. To better understand the molecular basis of the disease we ascertained blood and tumor samples from Guatemala and Venezuela and performed genomic characterization. We performed HPV typing and identified somatically mutated genes using exome and ultra-deep targeted sequencing with confirmation in samples from Mexico. Copy number changes were also assessed in the exome sequence. Cervical cancer cases in Guatemala and Venezuela have an average age-of-diagnosis of 50 years, and 5.6 children. Analysis of 675 tumors revealed activation of PIK3CA and other phosphatidyl inositol (PI3K)/AKT pathway genes in 31% of squamous carcinomas and 24% of adeno- and adenosquamous tumors, predominantly at two sites (E542K, E545K) in the helical domain of the PIK3CA gene. This distribution of PIK3CA mutations is distinct from most ot...