• 응용통계연구
• /
• 제22권1호
• /
• pp.115-127
• /
• 2009

The purpose of statistical analyses of array-CGH experiment data is to divide the whole genome into regions of equal copy number, to quantify the copy number in each region and finally to evaluate its significance of being different from two. Several statistical procedures have been proposed which include the circular binary segmentation, and a Gaussian based local regression for detecting break points (GLAD) by estimating a piecewise constant function. We propose in this note a penalized spline regression and its simultaneous confidence band(SCB) approach to evaluate the statistical significance of regions of genetic gain/loss. The region of which the simultaneous confidence band stays above 0 or below 0 can be considered as a region of genetic gain or loss. We compare the performance of the SCB procedure with GLAD and hidden Markov model approaches through a simulation study in which the data were generated from AR(1) and AR(2) models to reflect spatial dependence of the array-CGH data in addition to the independence model. We found that the SCB method is more sensitive in detecting the low level copy number alterations.

• 한국방송∙미디어공학회:학술대회논문집
• /
• 한국방송∙미디어공학회 2020년도 하계학술대회
• /
• pp.571-572
• /
• 2020

3D 디스플레이 산업에 있어서 홀로그램의 상용화는 여전히 많은 문제점을 가지고 있다. Computer Generated Hologram(CGH)은 홀로그램 분야 중에서도 3D 물체를 생성하는데 여러 가지 강점을 가지고 있지만 큰 해상도를 가진 CGH를 생성하는데 많은 연산시간이 걸려 상업화에 걸림돌이 되고 있다. 이 논문에서는 이를 해결하기 위하여 오목 렌즈 함수를 이용한 초 고해상도 CGH를 생성하는 알고리즘을 이용하여 초 고해상도 홀로그램을 생성하는 방법을 제안하였다. 초 고해상도 CGH를 생성하기 위하여 필요한 일반적인 방법으로 실제로 계산해야 될 CGH의 크기는 4 메가픽셀(2k X 2k) 수준의 저해상도로서, 저사양의 컴퓨터로서도 충분히 빠르고 부담 없이 계산해낼 수 있는 사이즈이다. 생성된 CGH로 Array를 형성한 후, 해당 위치에 알맞은 임의의 오목 렌즈 함수를 곱해줌으로서 임의의 크기 및 복원 거리를 가지는 초고해상도 CGH를 생성할 수 있음을 확인하였다.

• Journal of Genetic Medicine
• /
• 제5권1호
• /
• pp.65-68
• /
• 2008

염색체 말단부위의 결실, 혹은 중복 등의 재배열은 정신지체나 기형의 중요한 원인이 되며, 정신지체 환자 2,500명에서 5%미만으로 보고되고 있다. 그러나 일반적으로 행하여지는 핵형 분석으로는 미세한 염색체의 재배열을 정확히 설명하기 어렵다. 본 증례는 불균형 전좌를 가진 성인여성의 정확한 핵형 분석을 위해 말초혈액의 분석 시 기존의 세포유전학적인 방법에 분자유전학적인 방법을 함께 병행한 보고이다. 환자는 31세 여성으로 심각한 정신지체, 행동발달과 언어 발달 장애를 보였으며, 그 원인분석을 위해 Trypsin과 Giemsa를 이용한 GTG 염색법으로 핵형분석을 시행하였다. 그 결과, 46,XX,add(8)(p23.3)으로 확인되었으며, 기원을 확인하기 위하여 부모 염색체 검사를 통해 유전력의 여부를 확인하고, array CGH와 FISH를 시행하여 기원을 알 수 없는 염색체 조각의 기원을 확인한 결과 46,XX,der(8)t(8;13)(p23.3;q32.1)dn의 최종 핵형을 확인하였다. 따라서, FISH 또는 array-CGH 등의 분자유전학적 방법의 적절하고 적극적인 적용은 기존의 세포유전학적 방법을 보완하여, 환자의 정보를 빠르고 정확하게 보고하는데 매우 유용하고, 효과적인 방법이라 하겠다.

• Journal of Genetic Medicine
• /
• 제8권1호
• /
• pp.62-66
• /
• 2011

14q32.33을 포함한 14번 염색체 장완 결실은 드문 질환이다. 14번 염색체의 말단 결실은 여러 임상증상을 공통적으로 보일 수 있으나 결실 절단부 (breakpoint)에 따라 표현형이 다양하게 발생할 수 있다. 저자들은 경련을 동반한 5세 여아에서 array comparative genomic hybridization (array-CGH)와 fluorescence in situ hybridization (FISH) 방법을 이용하여 이전 보고에 비해 가장 작은 14q32.33부위의 0.33 Mb 크기의 말단 결실과 심하지 않은 표현형을 보이는 1례를 경험 하였기에 문헌고찰과 함께 보고하는 바이다.

• 한국유전체학회:학술대회논문집
• /
• 한국유전체학회 2004년도 The 13th Korea Genome Conference
• /
• pp.46.1-46.1
• /
• 2004

• 대한전자공학회:학술대회논문집
• /
• 대한전자공학회 2008년도 하계종합학술대회
• /
• pp.897-898
• /
• 2008

Array comparative genomic hybridization (aCGH) has been used to detect chromosomal regions of amplifications or deletions, which allows identification of new cancer related genes. As aCGH, a large-scale spatial data, contains significant amount of noises in its raw data, it has been an important research issue to segment genomic DNA regions to detect its true underlying copy number aberrations (CNAs). In this study, we focus on applying a segmentation method to multiple data sets. We compare two different threshold values for analyzing aCGH data with CBS method [1]. The proposed threshold values are p-value or $Q{\pm}1.5IQR$ and $Q{\pm}1.5IQR$.

• 디지털산업정보학회논문지
• /
• 제9권1호
• /
• pp.129-139
• /
• 2013

In this paper, we proposed a new hardware architecture for calculating digital holograms at high speed, and verified it with field programmable gate array (FPGA). First, we rearranged memory scheduling and algorithm of computer generated hologram (CGH), and then introduced pipeline technique into CGH process. Finally we proposed a high-performance CGH processor. The hardware was implemented for the target of FPGA, which calculates a unit region of holograms, and it was verified using a hardware environment of NI Inc. and a FPGA of Xilinx Inc. It can generate a hologram of $16{\times}16$ size, and it takes about 4 sec for generating a hologram of a $1,024{\times}1,024$ size, using 6K point sources.

• Clinical and Experimental Reproductive Medicine
• /
• 제39권2호
• /
• pp.52-57
• /
• 2012

Objective: During IVF, non-transferred embryos are usually selected for cryopreservation on the basis of morphological criteria. This investigation evaluated an application for array comparative genomic hybridization (aCGH) in assessment of surplus embryos prior to cryopreservation. Methods: First-time IVF patients undergoing elective single embryo transfer and having at least one extra non-transferred embryo suitable for cryopreservation were offered enrollment in the study. Patients were randomized into two groups: Patients in group A (n=55) had embryos assessed first by morphology and then by aCGH, performed on cells obtained from trophectoderm biopsy on post-fertilization d5. Only euploid embryos were designated for cryopreservation. Patients in group B (n=48) had embryos assessed by morphology alone, with only good morphology embryos considered suitable for cryopreservation. Results: Among biopsied embryos in group A (n=425), euploidy was confirmed in 226 (53.1%). After fresh single embryo transfer, 64 (28.3%) surplus euploid embryos were cryopreserved for 51 patients (92.7%). In group B, 389 good morphology blastocysts were identified and a single top quality blastocyst was selected for fresh transfer. All group B patients (48/48) had at least one blastocyst remaining for cryopreservation. A total of 157 (40.4%) blastocysts were frozen in this group, a significantly larger proportion than was cryopreserved in group A (p=0.017, by chi-squared analysis). Conclusion: While aCGH and subsequent frozen embryo transfer are currently used to screen embryos, this is the first investigation to quantify the impact of aCGH specifically on embryo cryopreservation. Incorporation of aCGH screening significantly reduced the total number of cryopreserved blastocysts compared to when suitability for freezing was determined by morphology only. IVF patients should be counseled that the benefits of aCGH screening will likely come at the cost of sharply limiting the number of surplus embryos available for cryopreservation.

• Genomics & Informatics
• /
• 제8권1호
• /
• pp.19-27
• /
• 2010

To discover genetic markers for autism spectrum disorder (ASD), we previously applied genome-wide BAC array comparative genomic hybridization (array-CGH) to 28 autistic patients and 62 normal controls in Korean population, and identified that chromosomal losses on 8p23.1 and on 17p11.2 are significantly associated with autism. In this study, we developed an 8.5K ASD-specific BAC array covering 27 previously reported ASD-associated CNV loci including ours and examined whether the associations would be replicated in 8 ASD patient cell lines of four different ethnic groups and 10 Korean normal controls. As a result, a CNV-loss on 8p23.1 was found to be significantly more frequent in patients regardless of ethnicity (p<0.0001). This CNV region contains two coding genes, DEFA1 and DEFA3, which are members of DEFENSIN gene family. Two other CNVs on 17p11.2 and Xp22.31 were also distributed differently between ASDs and controls, but not significant (p=0.069 and 0.092, respectively). All the other loci did not show significant association. When these evidences are considered, the association between ASD and CNV of DEFENSIN gene seems worthy of further exploration to elucidate the pathogenesis of ASD. Validation studies with a larger sample size will be required to verify its biological implication.

• Clinical and Experimental Reproductive Medicine
• /
• 제38권3호
• /
• pp.126-134
• /
• 2011

Preimplantation genetic diagnosis (PGD) is gradually widely used in prevention of gene diseases and chromosomal abnormalities. Much improvement has been achieved in biopsy technique and molecular diagnosis. Blastocyst biopsy can increase diagnostic accuracy and reduce allele dropout. It is cost-effective and currently plays an important role. Whole genome amplification permits subsequent individual detection of multiple gene loci and screening all 23 pairs of chromosomes. For PGD of chromosomal translocation, fluorescence $in-situ$ hybridization (FISH) is traditionally used, but with technical difficulty. Array comparative genomic hybridization (CGH) can detect translocation and 23 pairs of chromosomes that may replace FISH. Single nucleotide polymorphisms array with haplotyping can further distinguish between normal chromosomes and balanced translocation. PGD may shorten time to conceive and reduce miscarriage for patients with chromosomal translocation. PGD has a potential value for mitochondrial diseases. Preimplantation genetic haplotyping has been applied for unknown mutation sites of single gene disease. Preimplantation genetic screening (PGS) using limited FISH probes in the cleavage-stage embryo did not increase live birth rates for patients with advanced maternal age, unexplained recurrent abortions, and repeated implantation failure. Polar body and blastocyst biopsy may circumvent the problem of mosaicism. PGS using blastocyst biopsy and array CGH is encouraging and merit further studies. Cryopreservation of biopsied blastocysts instead of fresh transfer permits sufficient time for transportation and genetic analysis. Cryopreservation of embryos may avoid ovarian hyperstimulation syndrome and possible suboptimal endometrium.