• Communications for Statistical Applications and Methods
• /
• v.16 no.2
• /
• pp.309-315
• /
• 2009

We extended the results of Roy and Guria (2008) to multiple deletions in logistic regression models. Since single deletions may not exactly detect outliers or influential observations due to swamping effects and masking effects, it needs multiple deletions. We developed conditional deletion diagnostics which are designed to overcome problems of masking effects. We derived the closed forms for several statistics in logistic regression models. They give useful diagnostics on the statistics.

• Journal of Genetic Medicine
• /
• v.10 no.2
• /
• pp.99-103
• /
• 2013

Purpose: This study was designed to determine the frequency and echocardiographic findings of 22q11.2 deletions in fetuses with cardiac defects on fetal ultrasound or familial backgrounds of 22q11.2 deletions. Materials and methods: We retrospectively reviewed the medical and ultrasonographic records of 170 fetuses that underwent fluorescence in situ hybridization (FISH) analysis for chromosome 22q11.2 deletions between February 2001 and April 2013. Results: Among 145 fetuses with cardiac defects, six (4.1%) had 22q11.2 deletions. Deletions of 22q11.2 were detected in 6 (5%) of the 120 fetuses with conotruncal defects: 5 (8.9%) of 56 with tetralogy of Fallot (TOF) and 1 (5.9%) of 17 with double outlet right ventricle (DORV). No deletions were found in cases of pulmonary atresia, truncus arteriosus, right aortic arch, or transposition of the great arteries. No 22q11.2 deletions were found in non-conotruncal cardiac malformations. Among 25 fetuses with familial backgrounds of 22q11.2 deletions, one (4%) had a maternally inherited 22q11.2 deletion with no cardiac findings. Conclusion: Knowledge of the frequency and echocardiographic findings of 22q11.2 deletions might be helpful for prenatal genetic counseling. It is advisable to perform FISH analysis for 22q11.2 deletions in pregnancies exhibiting conotruncal cardiac defects such as TOF or DORV.

• Journal of applied mathematics & informatics
• /
• v.10 no.1_2
• /
• pp.111-118
• /
• 2002

We study the influence of observations on testing a linear hypothesis using single and multiple case-deletions. The change in the F-test statistic due to case-deletions is shown to be completely determined by two externally Studentized residuals. These residuals we used for investigating the outlyingness when there are linear constraints or not. An illustrative example is given. It shows the usefulness of case-deletions.

• Journal of Genetic Medicine
• /
• v.18 no.2
• /
• pp.110-116
• /
• 2021

Microdeletions of chromosome 22q11.2 are one of the most common microdeletions occurring in humans, and is known to be associated with a wide range of highly variable features. These deletions occur within a cluster of low copy repeats (LCRs) in 22q11.2, referred to as LCR22 A-H. DiGeorge (DGS)/velocardiofacial syndrome is the most prevalent form of a 22q11.2 deletions, caused by mainly proximal deletions between LCR22 A and D. As deletions of distal portion to the DGS deleted regions has been extensively studied, the recurrent distal 22q11.2 microdeletions distinct from DGS has been suggested as several clinical entities according to the various in size and position of the deletions on LCRs. We report a case of long-term follow-up of a female diagnosed with a 22q11.2 distal deletion syndrome, identified a deletion of 1.9 Mb at 22q11.21q11.23 (chr22: 21,798,906-23,653,963) using single nucleotide polymorphism array. This region was categorized as distal deletion type of 22q11.2, involving LCR22 D-F. She was born as a preterm, low birth weight to healthy non-consanguineous Korean parents. She showed developmental delay, growth retardation, dysmorphic facial features, and mild skeletal deformities. The patient underwent a growth hormone administration due to growth impairment without catch-up growth. While a height gain was noted, she had become overweight and was subsequently diagnosed with pre-diabetes. Our case could help broaden the genetic and clinical spectrum of 22q11.2 distal deletions.

• Communications for Statistical Applications and Methods
• /
• v.20 no.3
• /
• pp.217-223
• /
• 2013

Two influence diagnostic methods for the common mean model are proposed. First, an investigation of the influence of observations according to minor perturbations of the common mean model is made by adapting the local influence method which is based on the likelihood displacement. It is well known that the maximum likelihood estimates are in general sensitive to influential observations. Case-deletions can be a candidate for detecting influential observations. However, the maximum likelihood estimators are iteratively computed and therefore case-deletions involve an enormous amount of computations. An approximation by Newton's method to the maximum likelihood estimator obtained after a single observation was deleted can reduce much of computational burden, which will be treated in this work. A numerical example is given for illustration and it shows that the proposed diagnostic methods can be useful tools.

• Communications for Statistical Applications and Methods
• /
• v.23 no.3
• /
• pp.231-239
• /
• 2016

A graphical diagnostic method based on multiple case deletions in a regression context is introduced by using the sampling distribution of the difference between two least squares estimators with and without multiple cases. Principal components analysis plays a key role in deriving this diagnostic method. Multiple case deletions of test statistic are also considered when a new observation is fitted to a given regression model. The result is useful for detecting influential observations in econometric data analysis, for example in checking whether the consumption pattern at a later time is the same as the one found before or not, as well as for investigating the influence of cases in the usual regression model. An illustrative example is given.

• Investigative Magnetic Resonance Imaging
• /
• v.22 no.3
• /
• pp.158-167
• /
• 2018

Purpose: To investigate the surgical, perfusion, and molecular characteristics of glioblastomas which influence long-term survival after treatment, and to explore the association between MR perfusion parameters and the presence of MGMT methylation and 1p/19q deletions. Materials and Methods: This retrospective study was approved by our institutional review board. A total 43 patients were included, all with pathologic diagnosis of glioblastoma with known MGMT methylation and 1p/19q deletion statuses. We divided these patients into long-term (${\geq}60\;months$, n = 7) and short-term (< 60 months, n = 36) survivors, then compared surgical extent, molecular status, and rCBV parameters between the two groups using Fisher's exact test or Mann-Whitney test. The rCBV parameters were analyzed according to the presence of MGMT methylation and 1p/19q deletions. We investigated the relationship between the mean rCBV and overall survival using linear correlation. Multivariable linear regression was performed in order to find the variables related to overall survival. Results: Long-term survivors (100% [7 of 7]) demonstrated a greater percentage of gross total or near total resection than short-term survivors (54.5% [18 of 33]). A higher prevalence of 1p/19q deletions was also noted among the long-term survivors (42.9% [3 of 7]) than the short-term survivors (0.0% [0 of 36]). The rCBV parameters did not differ between the long-term and short-term survivors. The rCBV values were marginally lower in patients with MGMT methylation and 1p/19q deletions. Despite no correlation found between overall survival and rCBV in the whole group, the short-term survivor group showed negative correlation ($R^2=0.181$, P = 0.025). Multivariable linear regression revealed that surgical extent and 1p/19q deletions, but not rCBV values, were associated with prolonged overall survival. Conclusion: While preoperative rCBV and 1p/19q deletion status are related to each other, only surgical extent and the presence of 1p/19q deletion in GBM patients may predict long-term survival.

• Genomics & Informatics
• /
• v.17 no.4
• /
• pp.40.1-40.9
• /
• 2019

While studies aimed at detecting and analyzing indels or single nucleotide polymorphisms within human genomic sequences have been actively conducted, studies on detecting long insertions/deletions are not easy to orchestrate. For the last 10 years, the availability of long read data of human genomes from PacBio or Nanopore platforms has increased, which makes it easier to detect long insertions/deletions. However, because long read data have a critical disadvantage due to their relatively high cost, many next generation sequencing data are produced mainly by short read sequencing machines. Here, we constructed programs to detect so-called unmapped regions (UMRs, where no reads are mapped on the reference genome), scanned 40 Korean genomes to select UMR long deletion candidates, and compared the candidates with the long deletion break points within the genomes available from the 1000 Genomes Project (1KGP). An average of about 36,000 UMRs were found in the 40 Korean genomes tested, 284 UMRs were common across the 40 genomes, and a total of 37,943 UMRs were found. Compared with the 74,045 break points provided by the 1KGP, 30,698 UMRs overlapped. As the number of compared samples increased from 1 to 40, the number of UMRs that overlapped with the break points also increased. This eventually reached a peak of 80.9% of the total UMRs found in this study. As the total number of overlapped UMRs could probably grow to encompass 74,045 break points with the inclusion of more Korean genomes, this approach could be practically useful for studies on long deletions utilizing short read data.

• Journal of the Korea Convergence Society
• /
• v.8 no.5
• /
• pp.213-221
• /
• 2017

This study empirically investigates the relation between information quality measured by accruals quality and the KOSPI200 index rebalancing. The accruals quality is used for the proxy of information quality and is estimated by employing the Francis et al. (2005) model. The result shows that there is a statistically significant difference between additions group and deletions group. The average information quality of deletions group is substantially lower than that of additions group. In addition, the regression analysis shows that the relationship between accruals quality and a dummy variable for changes in the KOSPI200 index composition is negative and statistically significant. This result implies that additions to the KOSPI200 stock index improves information quality and relieves the information risk of firm which results in the amelioration of information asymmetry. On the other hand, deletions from the KOSPI200 index result in the deterioration of information quality. These results are consistent with Merton (1987).

• BMB Reports
• /
• v.37 no.5
• /
• pp.522-526
• /
• 2004

Prader-Willi (PWS) and Angelman (AS) are syndromes of developmental impairment that result from the loss of expression of imprinted genes in the paternal (PWS) or maternal (AS) 15q11-q13 chromosome. Diagnosis on a clinical basis is difficult in newborns and young infants; thus, a suitable molecular test capable of revealing chromosomal abnormalities is required. We used a variety of cytogenetic and molecular approaches, such as, chromosome G banding, fluorescent in situ hybridization, a DNA methylation test, and a set of chromosome 15 DNA polymorphisms to characterize a cohort of 27 PWS patients and 24 suspected AS patients. Molecular analysis enabled the reliable diagnosis of 14 PWS and 7 AS patients, and their classification into four groups: (A) 6 of these 14 PWS subjects (44%) had deletions of paternal 15q11-q13; (B) 4 of the 7 AS patients had deletions of maternal 15q11-q13; (C) one PWS patient (8%) had a maternal uniparental disomy (UPD) of chromosome 15; (D) the remaining reliably diagnoses of 7 PWS and 3 AS cases showed abnormal methylation patterns of 15q11-q13 chromosome, but none of the alterations shown by the above groups, although they may have harbored deletions undetected by the markers used. This study highlights the importance of using a combination of cytogenetic and molecular tests for a reliable diagnosis of PWS or AS, and for the identification of genetic alterations.