The near-seabed multichannel seismic exploration systems have yielded remarkable successes in marine geological disaster assessment,marine gas hydrate investigation,and deep-sea mineral exploration owing to their high...The near-seabed multichannel seismic exploration systems have yielded remarkable successes in marine geological disaster assessment,marine gas hydrate investigation,and deep-sea mineral exploration owing to their high vertical and horizontal resolution.However,the quality of deep-towed seismic imaging hinges on accurate source-receiver positioning information.In light of existing technical problems,we propose a novel array geometry inversion method tailored for high-resolution deep-towed multichannel seismic exploration systems.This method is independent of the attitude and depth sensors along a deep-towed seismic streamer,accounting for variations in seawater velocity and seabed slope angle.Our approach decomposes the towed line array into multiline segments and characterizes its geometric shape using the line segment distance and pitch angle.Introducing optimization parameters for seawater velocity and seabed slope angle,we establish an objective function based on the model,yielding results that align with objective reality.Employing the particle swarm optimization algorithm enables synchronous acquisition of optimized inversion results for array geometry and seawater velocity.Experimental validation using theoretical models and practical data verifies that our approach effectively enhances source and receiver positioning inversion accuracy.The algorithm exhibits robust stability and reliability,addressing uncertainties in seismic traveltime picking and complex seabed topography conditions.展开更多
A profile of shallow crustal velocity structure(1–2 km) may greatly enhance interpretation of the sedimentary environment and shallow tectonic deformation.Recent advances in surface wave tomography, using ambient noi...A profile of shallow crustal velocity structure(1–2 km) may greatly enhance interpretation of the sedimentary environment and shallow tectonic deformation.Recent advances in surface wave tomography, using ambient noise data recorded with high-density seismic arrays, have improved the understanding of regional crustal structure. As the interest in detailed shallow crustal structure imaging has increased, dense seismic array methods have become increasingly efficient. This study used a high-density seismic array deployed in the Xinjiang basin in southeastern China, to record seismic data, which was then processed with the ambient noise tomography method. The high-density seismic array contained 203 short-period seismometers, spaced at short intervals(～ 400 m). The array collected continuous records of ambient noise for 32 days. Data preprocessing,cross correlation calculation, and Rayleigh surface wave phase-velocity dispersion curve extraction, yielded more than 16,000 Rayleigh surface wave phase-velocity dispersion curves, which were then analyzed using the direct-inversion method. Checkerboard tests indicate that the shear wave velocity is recovered in the study area, at depths of 0–1.4 km,with a lateral image resolution of ～ 400 m. Model test results show that the seismic array effectively images a 50 m thick slab at a depth of 0–300 m, a 150 m thick anomalous body at a depth of 300–600 m, and a 400 m thick anomalous body at a depth of 0.6–1.4 km. The shear wave velocity profile reveals features very similar to those detected by a deep seismic reflection profile across the study area. This demonstrates that analysis of shallow crustal velocity structure provides high-resolution imaging of crustal features.Thus, ambient noise tomography with a high-density seismic array may play an important role in imaging shallow crustal structure.展开更多
High-resolution approaches such as multiple signal classification and estimation of signal parameters via rotational invariance techniques（ESPRIT） are currently employed widely in multibeam echo-sounder（MBES）syste...High-resolution approaches such as multiple signal classification and estimation of signal parameters via rotational invariance techniques（ESPRIT） are currently employed widely in multibeam echo-sounder（MBES）systems for sea floor bathymetry,where a uniform line array is also required.However,due to the requirements in terms of the system coverage/resolution and installation space constraints,an MBES system usually employs a receiving array with a special shape,which means that high-resolution algorithms cannot be applied directly.In addition,the short-term stationary echo signals make it difficult to estimate the covariance matrix required by the high-resolution approaches,which further increases the complexity when applying the high-resolution algorithms in the MBES systems.The ESPRIT with multiple-angle subarray beamforming is employed to reduce the requirements in terms of the signal-to-noise ratio,number of snapshots,and computational effort.The simulations show that the new processing method can provide better fine-structure resolution.Then a highresolution bottom detection（HRBD） algorithm is developed by combining the new processing method with virtual array transformation.The application of the HRBD algorithm to a U-shaped array is also discuss.The computer simulations and experimental data processing results verify the effectiveness of the proposed algorithm.展开更多
A fast separable approach based on a cross array is presented, which has coarsegrained parallelism. Its computational load is far less than that of the two-dimensional (2-D) direct processing method and other existing...A fast separable approach based on a cross array is presented, which has coarsegrained parallelism. Its computational load is far less than that of the two-dimensional (2-D) direct processing method and other existing separable approaches. In order to compensate for the performance degradation due to separable processing, two postprocessing schemes are also proposed. Some computer simulation results are provided for illustration in the end.展开更多
Objective Prader-Willi Sydrome （PWS） is a human disorder related to genomic imprinting defect on 15ql 1-13. It is characterized by a series of classic features such as hypotonia, hyperphagia, obesity, osteoporosis, ...Objective Prader-Willi Sydrome （PWS） is a human disorder related to genomic imprinting defect on 15ql 1-13. It is characterized by a series of classic features such as hypotonia, hyperphagia, obesity, osteoporosis, typical facial and body dysmorphosis, hypogonadism, mental and behaviour disorders. Our study was designed to precisely detect the microdeletions, which accounts for 65%-70% of the PWS. Methods Physical and laboratory examinations were firstly performed to diagnose PWS clinically, and to discover novel clinical features. Then the patient was screened with bisulfite-specific sequencing and precisely delineated through high-density array CGH. Results With the bisulfite-specific sequencing, the detected CpG island in the PWS critical region was found homozygously hypermethylated. Then with array CGH, a 2.22 Mb type II microdeletion was detected, covering a region from MKRN3, MAGEL2, NDN, PWRN2, PWRN1, Cl2orf2, SNURF-SNRPN, C/D snoRNAs, to distal of UBE3A. Conclusions Array CGH, after the fast screening of Bisulfite-specific sequencing, is a feasible and precise method to detect microdeletions in PWS patients. A novel feature of metacarpophalangeal joint rigidity was also presented, which is the first time reported in PWS.展开更多
The spatial resolution of a commercial two-dimensional(2D)ionization chamber(IC)array is limited by the size of the individual detector and the center-to-center distance between sensors.For dose distributions with are...The spatial resolution of a commercial two-dimensional(2D)ionization chamber(IC)array is limited by the size of the individual detector and the center-to-center distance between sensors.For dose distributions with areas of steep dose gradients,inter-detector dose values are derived by the interpolation of nearby detector readings in the conventional mathematical interpolation of 2D IC array measurements.This may introduce significant errors,particularly in proton spot scanning radiotherapy.In this study,by combining logfile-based reconstructed dose values and detector measurements with the Laplacian pyramid image blending method,a novel method is proposed to obtain a reformatted dose distribution that provides an improved estimation of the delivered dose distribution with high spatial resolution.Meanwhile,the similarity between the measured original data and the downsampled logfilebased reconstructed dose is regarded as the confidence of the reformatted dose distribution.Furthermore,we quantify the performance benefits of this new approach by directly comparing the reformatted dose distributions with 2D IC array detector mathematically interpolated measurements and original low-resolution measurements.The result shows that this new method is better than the mathematical interpolation and achieves gamma pass rates similar to those of the original low-resolution measurements.The reformatted dose distributions generally yield a confidence exceeding 95%.展开更多
Objective The quality of microarray data influences the accuracy of comparative genomic analyses to a large extent.To ensure that the results obtained by using an in situ synthesized microarray are accurate,data quali...Objective The quality of microarray data influences the accuracy of comparative genomic analyses to a large extent.To ensure that the results obtained by using an in situ synthesized microarray are accurate,data quality is to be assessed by evaluating the melting temperature (Tm) of probes,probability of false synthesis rates,and fragmentation of labeled targets.Methods DNA from the Yersinia pestis vaccine strain EV76 was used for microarray analyses.Microarray results were confirmed by PCR.Statistical and bioinformatics methods were employed to perform microarray data analyses and evaluation.Results Correlation coefficients of the three datasets were above 0.95 after two-time stripping and hybridization with a labeled DNA with the size of fragmentation being 200 bp-2 kb,which showed that the hybridization results were highly reproducible.Correlation coefficients were lower with the values ranging from 0.87 to 0.92 between the datasets generated from hybridization with different sizes of the labeled DNA fragment.For the relationship between Tm and signal intensity,there was a different distribution of Tm in the lowest 300 or 3 000 probes with a range of 70 ℃-72 ℃ and the highest 300 or 3 000 probes with a range of 72 ℃-74 ℃.Conclusion The results of this study suggest that the initial microarray design may affect the accuracy of final analyses and that the probe Tm and the size of the labeled fragment may be the two factors of the greatest importance.展开更多
A novel rotational invariance technique for blind estimates of direction of arrival (I)OA) and Doppler frequency with unknown array manifold due to array sensor uncertainties is proposed, taking Doppler frequency diff...A novel rotational invariance technique for blind estimates of direction of arrival (I)OA) and Doppler frequency with unknown array manifold due to array sensor uncertainties is proposed, taking Doppler frequency difference between a successive pulses as rotational parameter. The effectiveness of the new method is confirmed by computer simulation. Compared with the existing 2-D DOA-frequeucy estimate techniques, the computation load of the proposed method can be saved greatly.展开更多
To aim at the problem that the horizontal directivity index of the vector hy- drophone vertical array is not higher than that of a vector hydrophone, the high-resolution azimuth estimation algorithm based on the data ...To aim at the problem that the horizontal directivity index of the vector hy- drophone vertical array is not higher than that of a vector hydrophone, the high-resolution azimuth estimation algorithm based on the data fusion method was presented. The proposed algorithnl first employs MUSIC algorithm to estimate the azimuth of each divided sub-band signal, and then the estimated azimuths of multiple hydrophones are processed by using the data fusion technique. The high-resolution estimated result is achieved finally by adopting the weighted histogram statistics method. The results of the simulation and sea trials indicated that the proposed algorithm has better azimuth estimation performance than MUSIC algorithm of a single vector hydrophone and the data fusion technique based on the acoustic energy flux method. The better performance is reflected in the aspects of the estimation precision, the probability of correct estimation, the capability to distinguish multi-objects and the inhibition of the noise sub-bands.展开更多
We are reporting the longest disease-free interval ever published for colorectal cancer, using gene profiling to confirm the linkage of the primary and metastasis. This rare case reports on a patient with late recurre...We are reporting the longest disease-free interval ever published for colorectal cancer, using gene profiling to confirm the linkage of the primary and metastasis. This rare case reports on a patient with late recurrence of colorectal cancer in the lung 19 years after its initial diagnosis. We used high-resolution array CGH(aCGH) to analyze the genetic aberrations of both the primary rectal and the recurrent metastatic lung lesions. Interestingly, we found striking similarities between the two lesions, despite the 19 years disease-free interval.In addition, most of the genes that were previously reported to be associated with a high recurrence score showed copy number gains by aCGH in one or both lesions. Our findings suggest that aCGH may be a helpful tool in analyzing the origin of metastatic lesions and reflect the need for a better understanding of the characteristics of the rectal tumors with a late recurrence potential.展开更多
Background: Sporadic colorectal tumors probably carry genetic alterations that may be related to familiar clusters according to risk loci visualized by SNP arrays on normal tissues. The aim of the present study was th...Background: Sporadic colorectal tumors probably carry genetic alterations that may be related to familiar clusters according to risk loci visualized by SNP arrays on normal tissues. The aim of the present study was therefore to search for DNA regions (copy number variations, CNVs) as biomarkers associated to genetic susceptibility for early risk predictions of colorectal cancer. Such sequence alterations could provide additional information on phenotypic grouping of patients. Material and Methods: High resolution 105K oligonucleotide microarrays were used in search for CNV loci in DNA from tumor-free colon mucosa at primary operations for colon cancer in 60 unselected patients in comparison to DNA in buffy coat cells from 44 confirmed tumor-free and healthy blood donors. Array-detected CNVs were confirmed by Multiplex ligation-dependent probe amplification (MLPA). Results: A total number of 205 potential CNVs were present in DNA from colon mucosa. 184 (90%) of the 205 potential CNVs had been identified earlier in mucosa DNA from healthy individuals as reported to the Database of Genomic Variants. Remaining 21 (10%) CNVs were potentially novel sites. Two CNVs (3q23 and 10q21.1) were significantly related to colon cancer, but not confirmed in buffy coat DNA from the cancer patients. Conclusion: Our study reveals two CNVs that indicate increased risk for colon cancer;These DNA alterations may have? been acquired by colon stem cells with subsequent appearance among epithelial mucosa cells. Impact: Certain mucosa CNV alterations may indicate individual susceptibility for malignant transformation in relationship to intestinal toxins and bacterial growth.展开更多
Array comparative genomic hybridization （CGH） has been popularly used for analyzing DNA copy number variations in diseases like cancer. In this study, we investigated 82 sporadic samples from 49 breast cancer patien...Array comparative genomic hybridization （CGH） has been popularly used for analyzing DNA copy number variations in diseases like cancer. In this study, we investigated 82 sporadic samples from 49 breast cancer patients using 1-Mb resolution bacterial artificial chromosome （2GH arrays. A number of highly frequent genomic aberrations were discovered, which may act as ＂drivers＂ of tumor progression. Meanwhile, the genomic profiles of four ＂normal＂ breast tissue samples taken at least 2 cm away from the primary tumor sites were also found to have some genomic aberrations that recurred with high frequency in the primary tumors, which may have important implications for clinical therapy. Additionally, we performed class comparison and class prediction for various clinicopathological parameters, and a list of characteristic genomic aberrations associated with different clinicopathological phenotypes was compiled. Our study provides clues for further investigations of the underlying mechanisms of breast carcinogenesis.展开更多
基金supported by the special funds of Laoshan Laboratory(No.LSKJ202203604)the National Key Research and Development Program of China(No.2016 YFC0303901).
文摘The near-seabed multichannel seismic exploration systems have yielded remarkable successes in marine geological disaster assessment,marine gas hydrate investigation,and deep-sea mineral exploration owing to their high vertical and horizontal resolution.However,the quality of deep-towed seismic imaging hinges on accurate source-receiver positioning information.In light of existing technical problems,we propose a novel array geometry inversion method tailored for high-resolution deep-towed multichannel seismic exploration systems.This method is independent of the attitude and depth sensors along a deep-towed seismic streamer,accounting for variations in seawater velocity and seabed slope angle.Our approach decomposes the towed line array into multiline segments and characterizes its geometric shape using the line segment distance and pitch angle.Introducing optimization parameters for seawater velocity and seabed slope angle,we establish an objective function based on the model,yielding results that align with objective reality.Employing the particle swarm optimization algorithm enables synchronous acquisition of optimized inversion results for array geometry and seawater velocity.Experimental validation using theoretical models and practical data verifies that our approach effectively enhances source and receiver positioning inversion accuracy.The algorithm exhibits robust stability and reliability,addressing uncertainties in seismic traveltime picking and complex seabed topography conditions.
基金supported by the China Geological Survey Project“Deep Geological Survey of the Qin-Hang Belt”(No.DD20160082)the National Natural Science Foundation of China(No.41574048)
文摘A profile of shallow crustal velocity structure(1–2 km) may greatly enhance interpretation of the sedimentary environment and shallow tectonic deformation.Recent advances in surface wave tomography, using ambient noise data recorded with high-density seismic arrays, have improved the understanding of regional crustal structure. As the interest in detailed shallow crustal structure imaging has increased, dense seismic array methods have become increasingly efficient. This study used a high-density seismic array deployed in the Xinjiang basin in southeastern China, to record seismic data, which was then processed with the ambient noise tomography method. The high-density seismic array contained 203 short-period seismometers, spaced at short intervals(～ 400 m). The array collected continuous records of ambient noise for 32 days. Data preprocessing,cross correlation calculation, and Rayleigh surface wave phase-velocity dispersion curve extraction, yielded more than 16,000 Rayleigh surface wave phase-velocity dispersion curves, which were then analyzed using the direct-inversion method. Checkerboard tests indicate that the shear wave velocity is recovered in the study area, at depths of 0–1.4 km,with a lateral image resolution of ～ 400 m. Model test results show that the seismic array effectively images a 50 m thick slab at a depth of 0–300 m, a 150 m thick anomalous body at a depth of 300–600 m, and a 400 m thick anomalous body at a depth of 0.6–1.4 km. The shear wave velocity profile reveals features very similar to those detected by a deep seismic reflection profile across the study area. This demonstrates that analysis of shallow crustal velocity structure provides high-resolution imaging of crustal features.Thus, ambient noise tomography with a high-density seismic array may play an important role in imaging shallow crustal structure.
基金The National Natural Science Foundation of China under contract No.41706066the National Key R&D Program of China under contract No.2016YFC1400200the China-ASEAN Maritime Cooperation Fund
文摘High-resolution approaches such as multiple signal classification and estimation of signal parameters via rotational invariance techniques（ESPRIT） are currently employed widely in multibeam echo-sounder（MBES）systems for sea floor bathymetry,where a uniform line array is also required.However,due to the requirements in terms of the system coverage/resolution and installation space constraints,an MBES system usually employs a receiving array with a special shape,which means that high-resolution algorithms cannot be applied directly.In addition,the short-term stationary echo signals make it difficult to estimate the covariance matrix required by the high-resolution approaches,which further increases the complexity when applying the high-resolution algorithms in the MBES systems.The ESPRIT with multiple-angle subarray beamforming is employed to reduce the requirements in terms of the signal-to-noise ratio,number of snapshots,and computational effort.The simulations show that the new processing method can provide better fine-structure resolution.Then a highresolution bottom detection（HRBD） algorithm is developed by combining the new processing method with virtual array transformation.The application of the HRBD algorithm to a U-shaped array is also discuss.The computer simulations and experimental data processing results verify the effectiveness of the proposed algorithm.
文摘A fast separable approach based on a cross array is presented, which has coarsegrained parallelism. Its computational load is far less than that of the two-dimensional (2-D) direct processing method and other existing separable approaches. In order to compensate for the performance degradation due to separable processing, two postprocessing schemes are also proposed. Some computer simulation results are provided for illustration in the end.
基金supported by grants from National 973 Program(2006CB503901)Shanghai Key Laboratory of Diabetes Mellitus(08DZ2230200)+1 种基金Major Program of Shanghai Municipality for Basic Research(08dj 1400601)Program for Outstanding Medical Academic Leader in Shanghai (LJ06010).
文摘Objective Prader-Willi Sydrome （PWS） is a human disorder related to genomic imprinting defect on 15ql 1-13. It is characterized by a series of classic features such as hypotonia, hyperphagia, obesity, osteoporosis, typical facial and body dysmorphosis, hypogonadism, mental and behaviour disorders. Our study was designed to precisely detect the microdeletions, which accounts for 65%-70% of the PWS. Methods Physical and laboratory examinations were firstly performed to diagnose PWS clinically, and to discover novel clinical features. Then the patient was screened with bisulfite-specific sequencing and precisely delineated through high-density array CGH. Results With the bisulfite-specific sequencing, the detected CpG island in the PWS critical region was found homozygously hypermethylated. Then with array CGH, a 2.22 Mb type II microdeletion was detected, covering a region from MKRN3, MAGEL2, NDN, PWRN2, PWRN1, Cl2orf2, SNURF-SNRPN, C/D snoRNAs, to distal of UBE3A. Conclusions Array CGH, after the fast screening of Bisulfite-specific sequencing, is a feasible and precise method to detect microdeletions in PWS patients. A novel feature of metacarpophalangeal joint rigidity was also presented, which is the first time reported in PWS.
文摘The spatial resolution of a commercial two-dimensional(2D)ionization chamber(IC)array is limited by the size of the individual detector and the center-to-center distance between sensors.For dose distributions with areas of steep dose gradients,inter-detector dose values are derived by the interpolation of nearby detector readings in the conventional mathematical interpolation of 2D IC array measurements.This may introduce significant errors,particularly in proton spot scanning radiotherapy.In this study,by combining logfile-based reconstructed dose values and detector measurements with the Laplacian pyramid image blending method,a novel method is proposed to obtain a reformatted dose distribution that provides an improved estimation of the delivered dose distribution with high spatial resolution.Meanwhile,the similarity between the measured original data and the downsampled logfilebased reconstructed dose is regarded as the confidence of the reformatted dose distribution.Furthermore,we quantify the performance benefits of this new approach by directly comparing the reformatted dose distributions with 2D IC array detector mathematically interpolated measurements and original low-resolution measurements.The result shows that this new method is better than the mathematical interpolation and achieves gamma pass rates similar to those of the original low-resolution measurements.The reformatted dose distributions generally yield a confidence exceeding 95%.
基金supported by a grant from the National High Technology Research and Development Program of China(863 Program,No. 2006AA2Z4A7)
文摘Objective The quality of microarray data influences the accuracy of comparative genomic analyses to a large extent.To ensure that the results obtained by using an in situ synthesized microarray are accurate,data quality is to be assessed by evaluating the melting temperature (Tm) of probes,probability of false synthesis rates,and fragmentation of labeled targets.Methods DNA from the Yersinia pestis vaccine strain EV76 was used for microarray analyses.Microarray results were confirmed by PCR.Statistical and bioinformatics methods were employed to perform microarray data analyses and evaluation.Results Correlation coefficients of the three datasets were above 0.95 after two-time stripping and hybridization with a labeled DNA with the size of fragmentation being 200 bp-2 kb,which showed that the hybridization results were highly reproducible.Correlation coefficients were lower with the values ranging from 0.87 to 0.92 between the datasets generated from hybridization with different sizes of the labeled DNA fragment.For the relationship between Tm and signal intensity,there was a different distribution of Tm in the lowest 300 or 3 000 probes with a range of 70 ℃-72 ℃ and the highest 300 or 3 000 probes with a range of 72 ℃-74 ℃.Conclusion The results of this study suggest that the initial microarray design may affect the accuracy of final analyses and that the probe Tm and the size of the labeled fragment may be the two factors of the greatest importance.
基金Supported by the National Natural Science Foundation of China
文摘A novel rotational invariance technique for blind estimates of direction of arrival (I)OA) and Doppler frequency with unknown array manifold due to array sensor uncertainties is proposed, taking Doppler frequency difference between a successive pulses as rotational parameter. The effectiveness of the new method is confirmed by computer simulation. Compared with the existing 2-D DOA-frequeucy estimate techniques, the computation load of the proposed method can be saved greatly.
基金the leaders of the State Key Laboratory of Acoustics Institute of Acoustics,Chinese Academy of Sciences,for their project support
文摘To aim at the problem that the horizontal directivity index of the vector hy- drophone vertical array is not higher than that of a vector hydrophone, the high-resolution azimuth estimation algorithm based on the data fusion method was presented. The proposed algorithnl first employs MUSIC algorithm to estimate the azimuth of each divided sub-band signal, and then the estimated azimuths of multiple hydrophones are processed by using the data fusion technique. The high-resolution estimated result is achieved finally by adopting the weighted histogram statistics method. The results of the simulation and sea trials indicated that the proposed algorithm has better azimuth estimation performance than MUSIC algorithm of a single vector hydrophone and the data fusion technique based on the acoustic energy flux method. The better performance is reflected in the aspects of the estimation precision, the probability of correct estimation, the capability to distinguish multi-objects and the inhibition of the noise sub-bands.
基金Supported by Lombardi Comprehensive Cancer Center,Georgetown University Medical Center,Washington,DC,United States
文摘We are reporting the longest disease-free interval ever published for colorectal cancer, using gene profiling to confirm the linkage of the primary and metastasis. This rare case reports on a patient with late recurrence of colorectal cancer in the lung 19 years after its initial diagnosis. We used high-resolution array CGH(aCGH) to analyze the genetic aberrations of both the primary rectal and the recurrent metastatic lung lesions. Interestingly, we found striking similarities between the two lesions, despite the 19 years disease-free interval.In addition, most of the genes that were previously reported to be associated with a high recurrence score showed copy number gains by aCGH in one or both lesions. Our findings suggest that aCGH may be a helpful tool in analyzing the origin of metastatic lesions and reflect the need for a better understanding of the characteristics of the rectal tumors with a late recurrence potential.
基金Supported in parts by grants from the Swedish Cancer Society(CAN 2010/255),the Swedish Research Council(08712),Tore Nilson Foundation,Assar Gabrielsson Foundation(AB Volvo),Jubileumskliniken Foundation,IngaBritt&Arne Lundberg Research Foundation,Swedish and Gothenburg Medical Societies and the Medical Faculty,University of Gothenburg,VGR 19/00,1019/00.
文摘Background: Sporadic colorectal tumors probably carry genetic alterations that may be related to familiar clusters according to risk loci visualized by SNP arrays on normal tissues. The aim of the present study was therefore to search for DNA regions (copy number variations, CNVs) as biomarkers associated to genetic susceptibility for early risk predictions of colorectal cancer. Such sequence alterations could provide additional information on phenotypic grouping of patients. Material and Methods: High resolution 105K oligonucleotide microarrays were used in search for CNV loci in DNA from tumor-free colon mucosa at primary operations for colon cancer in 60 unselected patients in comparison to DNA in buffy coat cells from 44 confirmed tumor-free and healthy blood donors. Array-detected CNVs were confirmed by Multiplex ligation-dependent probe amplification (MLPA). Results: A total number of 205 potential CNVs were present in DNA from colon mucosa. 184 (90%) of the 205 potential CNVs had been identified earlier in mucosa DNA from healthy individuals as reported to the Database of Genomic Variants. Remaining 21 (10%) CNVs were potentially novel sites. Two CNVs (3q23 and 10q21.1) were significantly related to colon cancer, but not confirmed in buffy coat DNA from the cancer patients. Conclusion: Our study reveals two CNVs that indicate increased risk for colon cancer;These DNA alterations may have? been acquired by colon stem cells with subsequent appearance among epithelial mucosa cells. Impact: Certain mucosa CNV alterations may indicate individual susceptibility for malignant transformation in relationship to intestinal toxins and bacterial growth.
基金supported by the Danish Cancer Soci-ety through the budget of the Institute of Cancer Biol-ogy and by grants from the Danish Medical Research Council, the Natural and Medical Sciences Committee of the Danish Cancer Society, Novo Nordisk, the John and Birthe Meyer Foundation, the Solar Fonden, the Stensbygaard Fonden, the Kai Langeog Gundhild Kai Lange Fond, the will of Edith Stern, and the "Race Against Breast Cancer" ProjectThe support of the Marketing Department at the Danish Cancer Society is greatly appreciatedsupported by a project grant from the Hi-Tech Research and Development Program of China (2006AA02A301)
文摘Array comparative genomic hybridization （CGH） has been popularly used for analyzing DNA copy number variations in diseases like cancer. In this study, we investigated 82 sporadic samples from 49 breast cancer patients using 1-Mb resolution bacterial artificial chromosome （2GH arrays. A number of highly frequent genomic aberrations were discovered, which may act as ＂drivers＂ of tumor progression. Meanwhile, the genomic profiles of four ＂normal＂ breast tissue samples taken at least 2 cm away from the primary tumor sites were also found to have some genomic aberrations that recurred with high frequency in the primary tumors, which may have important implications for clinical therapy. Additionally, we performed class comparison and class prediction for various clinicopathological parameters, and a list of characteristic genomic aberrations associated with different clinicopathological phenotypes was compiled. Our study provides clues for further investigations of the underlying mechanisms of breast carcinogenesis.
